Title Deriviations (and Homages and such)

Or just shared. Some of them could just be coincidences.
EDITED 5/3/2015 Decided to include other series as well. 

STAR WARS
TV Series
The Clone Wars (2008)

Season One

Season Two

Season Three

Season Four

Season Five

   17. Sabotage-- film by Alfred Hitchcock 

   18. The Jedi Who Knew Too Much-- homage to The Man Who Knew Too Much film by Alfred Hitchcock 

   19. To Catch a Jedi-- homage to To Catch a Thief film by Alfred Hitchcock

   20. The Wrong Jedi-- homage to The Wrong Man film by Alfred Hitchcock

Rebels (2014)
TRANSFORMERS
TV Series
The Transformers (1984)

   24. A Decepticon Raider in King Arthur's Court-- homage to A Connecticut Yankee in King Arthur's Court novel by Mark Twain

   20. The Big Broadcast of 2006-- The Big Broadcast film series by Frank Tuttle

Beast Wars (1996)
Beast Machines (1999)

   16. Prometheus Unbound-- incomplete play by Aeschylus
   18. A Wolf in the Fold-- reference to Star Trek episode "Wolf in the Fold" ?
   23. Spark of Darkness-- homage to Heart of Darkness novella by Joseph Conrad
   24. The Downward Spiral-- album and song by Nine Inch Nails  

Animated (2007)

   9. Along Came a Spider-- nursery rhyme or the novel by James Patterson

   10. Sound and Fury-- line from Shakespeare's Macbeth

   23. A Fistful of Energon-- homage to A Fistful of Dollars film by Sergio Leone

   34. Where Is Thy Sting?-- phrase from the Bible

   35. Five Servos of Doom-- possible homage to Five Fingers of Death film by Chang-hwa Chung

Prime (2010)
Rescue Bots (2011)

   2. Under Pressure -- song by David Bowie and Queen

   6. Walk on the Wild Side -- title of several different works
   8. Four Bots and a Baby -- homage to Three Men and a Baby film by Leonard Nimoy

   26. Bot to the Future -- homage to Back to the Future film by Robert Zemeckis

   39. The Island of Misfit Tech -- homage to the Island of Misfit Toys from Rudolph the Red-Nosed Reindeer.

   53. Land Before Prime -- homage to The Land Before Time film by Don Bluth

   61. Bot-Tastic Voyage -- homage to Fantastic Voyage film by Richard Fleischer
   65. All Bots Great and Small -- homage to All Creatures Great and Small novel by James Harriot
   76. I Have Heard the Robots Singing -- based on a line from The Love Song of J. Alfred Prufrock by T.S. Eliot ("I have heard the mermaids singing, each to each.")
   99. Cody's 11 -- homage to Ocean's 11 film by Lewis Milestone

Robots in Disguise (2015)

   11. Adventures in Bumblebee-sitting! -- homage to Adventures in Babysitting film by Chris Columbus
   17. One of Our Mini-Cons Is Missing -- homage to One of Our Aircraft Is Missing film by Michael Powell and Emeric Pressburger

Comics
Marvel Comics

G1 US

   #16: Plight of the Bumblebee!-- homage to "Flight of the Bumblebee" by Nikolai Rimsky-Korsakov

   #23: Decepticon Graffiti!-- homage to American Graffiti film by George Lucas

   #31: Buster Witwicky and the Car Wash of Doom-- homage to Indiana Jones and the Temple of Doom film by Steven Spielberg

   #52: Guess Who the Mecannibals Are Having for Dinner?-- possible homage to Guess Who's Coming to Dinner

   #54: King Con!-- homage to King Kong

   #63: Kings of the Wild Frontier-- lyrics to "The Ballad of Davy Crockett" by The Wellingtons
G1 UK

   #18-21: Raiders of the Last Ark-- homage to Raiders of the Lost Ark film by Steven Speilberg
   Annual 1991: The Magnificent Six!-- homage to The Magnificent Seven by John Stuges

G.I. Joe and the Transformers

   #1: Blood on the Tracks-- album by Bob Dylan

Headmasters

Dreamwave Productions

Generation One vol.3

   #4: Runnin' with the Devil-- song by Van Halen
Micromasters
   #1: Destined for Nothing-- song by Bad Religion
   #2: The Grey Race-- album by Bad Religion
   #3: Recipe for Hate-- album by Bad Religion
   #4: Victims of the Revolution-- song by Bad Religion
   [Someone must really like Bad Religion]

IDW Publishing

IDW G1

Spotlight
   Trailcutter: The Reluctant Specialist-- homage to The Reluctant Fundamentalist by Mohsin Hamid
All Hail Megatron
   #15: Everything in Its Right Place-- song by Radiohead
   #16: The Man of Steel-- reference to Superman, probably.
The Transformers
   #1: ...For All Mankind-- taken from a quote on the plaque left on the moon by Apollo 11

   #2: New Arrivals, Old Encounters-- story by Brian Aldiss

   #3: A Rude Awakening-- story by Brian Aldiss

   #4: Seasons in Flight-- story by Brian Aldiss

   #5: Enemies of the System-- story by Brian Aldiss

   #6: Earthworks-- story by Brian Aldiss
   #7: All His Engines-- quote from John Milton's Paradise Lost
   #9: The Land Ironclads-- short story by H.G. Wells
   #10: Ranks of Bronze-- novel by David Drake
   #11: Hawk Among the Sparrows-- novel by Dean McLaughlin
   #12: All My Sins Remembered-- quote from Shakespeare's Hamlet
   #13: Heart Like a Wheel-- title of several different works

   #14: The Demolished Man-- novel by Albert Bester

   #15: Altered Carbon-- novel by Richard K. Morgan

   #16: Woken Furies-- novel by Richard K. Morgan

   #17: Burning Chrome-- short story by William Gibson

   #18: Enemy Mine-- novella by Barry B. Longyear

   #19: The Stars My Destination-- novel by Albert Bester

   #20: Out of the Silent Planet-- novel by C.S. Lewis

   #21: Orphans of the Helix-- short story by Dan Simmons

   #24: Lamentations-- Book of the Bible
   #26: Numbers-- Book of the Bible

   #27: Only Forward-- novel by Michael Marshall Smith
   #28: Kings-- Book of the Bible

   #29: A Second Chance at Eden-- anthology by Peter F. Hamilton
   #30: Genesis-- Book of the Bible
Bumblebee
   #1: The Hanging Sword-- Greek story about Damocles
   #2: The Impossible Knot-- Greek about the Gordian Knot
   #3: The Gift Horse-- Greek myth about the Trojan horse
   #4: Wings of Wax-- Greek myth about Icarus
Ironhide

More than Meets the Eye
   #1-3: Liars, A to D-- "Liars, A to E" by Dexy's Midnight Runners

   #6: Interiors-- film by Woody Allen
   #8: Who's Afraid of the DJD?-- "Who's Afraid of the Big Bad Wolf?"

   #13: Cybertronian Homesick Blues-- "Subterranean Homesick Blues" by Bob Dylan

   #15: Under Cold Blue Stars-- album by Josh Rouse
   #17-21: Remain in Light-- album by Talking Heads
   #19: The Divided Self-- work by R.D. Laing
   #20: Arm the Lonely-- song by Savoy Grand
   #26: Burning Bright-- "The Tyger" poem by William Blake

   #28-30: World, Shut Your Mouth-- album by Julian Cope
   #29: Words Hang in the Air-- song by The Ladybug Transistor

   #33: The Road Not Taken-- poem by Robert Frost

   #35-38: Elegant Chaos-- "An Elegant Chaos" by Julian Cope
   #39: The Permanent Revolution-- term from Marxist theory
   #40: Our Steps Will Always Rhyme-- "Hey, That's No Way to Say Goodbye" by Leonard Cohen
   #41: The Sensuous Frame-- line from In Memoriam A.H.H., poem by Alfred, Lord Tennyson
   #43: The One Where They Go To Earth-- homage to the episode titles of Friends

   #48-49: Speak, Memory-- novel by Vladimir Nabokov
   #50-55: The Dying of the Light-- all quotes taken from poem by Dylan Thomas
      -How Bright Their Frail Deeds
      -The Sun in Flight
      -Your Fierce Tears
      -At Close of Day
      -Rage, Rage
      -Do Not Go Gentle
Robots in Disguise
   #1: The Autonomy Lesson-- issue of Swamp Thing by Alan Moore
   #9: Night and the City-- novel by Gerald Kirsh
   #28: Hello Cruel World-- song by Mark Oliver Everett (possibly)
   #29: Detonation Boulevard-- song by Sisters of Mercy
   #31: Full Fathom Five-- quote from Shakespeare's The Tempest
   #32: I Dream of Wires-- song by Gary Numan
   #35: Signals, Calls, and Marches-- album by Mission of Burma
   #36: Vs.-- album by Mission of Burma
   #37: ONoffON-- album by Mission of Burma
   #38: The Obliterati-- album by Mission of Burma
   #42: Now and On Earth-- novel by Jim Thompson
   #43: South of Heaven-- novel by Jim Thompson
   #44: The Transgressors-- novel by Jim Thompson
   #45: The Nothing Man-- novel by Jim Thompson 
   #50: Once Upon a Time on Earth-- homage to Once Upon a Time in the West.
   #53: It's Beginning To And Back Again-- album by Wire
   #54: As Above...So Below-- Hermetic phrase from the Emerald Tablet
   #55: No Fair Fights-- song by Prick
   #56-57: White Light/White Heat-- album by The Velvet Underground
Dark Cybertron
   #2: ...And the Damage Done-- "The Needle and the Damage Done" by Neil Young
Till All Are One
   #10: The Price of You-- song by NoComply
Revolution
   #1: Concord Hymn-- poem by Ralph Waldo Emerson
   #2: The Divine Source of Liberty-- poem by Samuel Adams
   #3: O Ship of State-- poem by Henry Wadsworth Longfellow
   #4: The New Colossus-- poem by Emma Lazarus
   #5: Valley Forge-- poem by Thomas Buchanan Read
Optimus Prime
   #1-6: New Cybertron-- all lyrics from "Babel" by Covenant
      -To Walk Among the Chosen
      -A Lonely Pillar on the Plain
      -Behind My Bleeding Back
      -Dance Among the Shadows
      -Future Glories Lost
      -Feel Safe Without Regrets
   #7: The Next Day, and the Next-- song by David Bowie
Lost Light
   #4: Bad Moon Rising-- song by Creedence Clearwater Revival
   #8: An Axe to Break the Ice-- lyrics from "Ashes to Ashes" by David Bowie
   #22: The Return of the King-- third novel of The Lord of the Rings series by J.R.R. Tolkien

Other G1

Transformers vs. G.I. Joe

   #1: I Saw Three Ships-- English Christmas carol

   #5: Everybody Hates Metroplex-- homage to Everybody Loves Raymond 

Text Stories

Fun Publications

TransTech

   Withered Hope-- song by They Might Be Giants.

   I, Lowtech-- homage to I, Robot, story collection by Isaac Asimov.

Shattered Glass

   Dungeons & Dinobots-- homage to Dungeons & Dragons

   Eye in the Sky-- possible reference to the song by The Alan Parsons Project

   Blitzwing Bop-- homage to "Blitzkrieg Bop" by The Ramones.

The Essential Guide to Transformers Regenerated

TABLE OF CONTENTS

Characters

Organized by continuity of origin.

-

Generation One

   Year 1 (1984)

   Year 2 (1985)

   Year 3 (1986)

   Year 4 (1987)

   Year 5 (1988)

   Year 6 (1989) + Year 7 (1990)

   European Years (1991-1993) + Generation Two (1993-1995)

   21st Century

Beast Era + Robots in Disguise
Unicron Trilogy

Movies

Animated + Aligned

Original Characters

Locations

Title Drops

Spoiler alert, just in case.

STAR WARS
TRANSFORMERS
Films

Live-action film series

    "Better call the city! We've got a blown transformer!"- Ron Witwicky (first movie)
    "Revenge... is mine."- The Fallen (second movie)

Shows
The Transformers
Beast Wars

Season One

    "So for now, let the battle be here, on this strange primitive world. And let it be called... Beast Wars!"- Optimus Primal (Episode 2)

    "It seems as though you have built a better mousetrap."- Dinobot (Episode 9)

Season Two

Season Three

Beast Machines

Animated

Season One

Season Two

Season Three

Prime

Season One
    "His sick mind's still at work." (Episode 13)

    "The fact is Starscream, despite your treachery, I've allowed you to carry on this long because I took a certain delight in following your string of failures. But you've finally become tiresome, predictable... you've hit rock bottom." (Episode 19)
    "Stronger, faster, studlier." (Episode 22)

Season Two

    "The human factor did indeed tip the scales... in favor of my enemies." (Episode 45)

    "Megatron certainly knows how to patch things up."(Episode 50)

Season Three
    "Does Wheeljack not comprehend the chain of command?" (Episode 58) 

Comics

IDW Publishing

Spotlight (various, 2006)
   "Surely I can't be the only one who's heard of Omega's Conundrum... 'When something ceases to be observed, how can we be sure it continues to exist?'" (Spotlight: Orion Pax)
More than Meets the Eye (James Roberts, 2012)

    "But all good things must come to an end, and if there's one thing I've learned, it's how to say goodbye and mean it." (#1)

    "I look around me and I'm embarrassed. I've never seen such a sorry bunch of has-beens and hangers-on." (#2)
    "There's no before or after to our 'relationship': I'm still going to kill you. All that changes is the manner of your death, which becomes more elaborate and protracted by the day." (#12) 

    "The House of Ambus has a very distinct facial insignia...." (#18)
    "Rung looked up from the table at the sound of breaking glass." (#21 short story)
    "Little victories, Rewind. Little victories." (#22)

    "Towards Peace. Your auto-biography." - Rung (#28)

    "Information carries weight. It's not corporeal, but it has presence. It can be felt. It hangs in the air like--like words." (#29) 
    "Just remember the four rules: no guns, no swords, no briefcases, and no telling Ultra Magnus." (#50)

Robots in Disguise (John Barber, 2012)
   "They're making a mistake... we fliers need to stick together." (#3)

Dark Cybertron
   "He said he needed an army in case the dead were not enough." (#7)
   "And to defend my becoming, from across the universe comes my army of Ammonites-- seventy billion strong." (#10)
Optimus Prime (John Barber, 2016)
   "Then, when we finally discovered Cybertron... we came upon a surfeit of Primes." (#15)
   "Thus, today... I find myself on another world in another mine." (#16)
   "I'm getting used to the unexpected... but I honestly didn't expect the ground to literally fall out from underneath me." (#17)
   "The hallowing is at hand." (#19)
   "I made an unforgivable mistake, Windblade." (#21)
Lost Light (James Roberts, 2016)

HARRY POTTER

--Books--

MIDDLE-EARTH

--Books--

--Films--

The Lord of the Rings

   "There is only one Lord of the Rings. Only one who can bend it to his will. And he does not share power!" - Gandalf

   "You shall be the Fellowship of the Ring!" - Elrond

   "Who now dares to stand against the union of the two towers?" - Saruman

   "It is not your place to deny the return of the king, steward!" - Gandalf

The Hobbit

   "Once, it was the kingdom of Dale. Now, it is a ruin. The desolation of Smaug." - Balin

BIONICLE
MY STORIES

Star Wars

Transformers
Regenerated

The Unicron Saga

    "We are the Heralds of Unicron. And our day of reckoning has come." (#14)

The Lost Light Chronicles
    "Help us create a better tomorrow for you and him." (#2)
The Prime Wars

Pax Cybertronia

Beyond Imagination

--Bionicle--

Transformers IDW Soundtracks

A list of all the song picks by MTMTE writer James Roberts for each issue (as well as for some characters).
Recently other IDW writers have taken up this practice, albeit not as regularly as Roberts.

James Roberts

More than Meets the Eye / Lost Light

Season One
   "Lost Coastlines" by Okkervil River
Liars, A to D Part 1: How to Say Goodbye and Mean It

   "Across the Universe" by Fiona Apple

   "Absent Friends" by The Divine Comedy

Liars, A to D Part 2: Hangers On

   "Calendar Girl" by Stars

   "Bloodbuzz Ohio" by The National

Liars, A to D Part 3: The Chaos of Warm Things

   "Love Love Love" by The Mountain Goats

   "Tonight We Fly" by The Divine Comedy

Life After the Big Bang

   "The Next Life" by Suede

   "Smokers Outside the Hospital Doors" by Editors

How Ratchet Got His Hands Back

   "Get Me Away From Here, I'm Dying" by Belle & Sebastian

   "Carries On" by Edward Sharpe and the Magnetic Zeros

   "City Sickness" by Thundersticks

Interiors

   "Sinister in a State of Hope" by Loney, Dear

   "A Good Man Is Easy to Kill" by Beulah

   "Easter Parade" by Emmy the Great

Scavengers (Part 1): Rules of Disengagement 

   "My Year in Lists" by Los Campesinos!

Primus: You, Me, and Other Revelations

   "Nothing Lasts Forever" by Echo & the Bunnymen 

   "For the Dead" by Gene

   "Too Late to Die Young" by Departure Lounge

Scavengers (Part 2): Who's Afraid of the DJD?

   "Die" by Iron & Wine

   "Do You Realize" by The Flaming Lips

Shadowplay

   "Comforting Sounds" by Mew
Shadowplay, Part 1: Post Hoc

   "Our Hearts Burn Like Damp Matches" by The Leisure Society

   Eternal Sunshine of the Spotless Mind theme by Jon Brion

Shadowplay, Part 2: Patternism

   "Action/Reaction" by Choir of Young Believers

   "Traffic Music" by Hjaltalin

Shadowplay (Conclusion): An Intimate Beheading

   "No Fear of Falling" by I Am Kloot

   "Atmosphere" by Joy Division

   "Plainsong" by The Cure

Before & After

   "Airbag" by Radiohead

   "Prelude for Time Feelers" by Eluvium

Cybertronian Homesick Blues
   "Now My Heart Is Full" by Morrissey
   "Subterranean Homesick Blues" by Bob Dylan
   "The Underdogs" by Rialto
   "The Good Old Days" by The Lodger
   "The Man Who Loved Beer" by David Byrne
   "Pamplona" by Pelle Carlberg
   "Lonely Hearts Still Beat the Same" by The Research
   "Last Night I Nearly Died (But I Woke Up Just In Time)" by Duke Special
   "It's Not the End of the World?" by Super Furry Animals
   "Bar Italia" by Pulp

Remembrance Day

   "The Fear" by Pulp

   "A Song From Under the Floorboards" by Magazine

   "Born of Frustration" by James

Under Cold Blue Stars

   "The First of the Gang to Die" by Morrissey 

   "The Mercy Seat" by Johnny Cash

   "Brothers and Sisters" by Duel

The Gloaming
   "Your Funny Uncle" by Pet Shop Boys
   "Holes" by Mercury Rev
   "Tracy" by Mogwai
   "Les Jour Tristes" by Neil Hannon & Yann Tiersen
   "The Sadness of Things" by Momus
   "Embers" by Byrne
   "Run" by Snow Patrol
   "Lullaby" by Arco

Remain in Light

   "A Dazzling End" by Murray Gold 

   "The Universal" by Blur
Remain in Light 1 of 5: The Fecund Moon

   "Heaven" by Talking Heads

   "A Comet Appears" by The Shins

Remain in Light 2 of 5: House of Ambus

   "Winterlight" by Clearlake

   "El Presidente" by Drugstore

   "Afterglow" by Holm

Remain in Light 3 of 5: The Divided Self
   n/a

Remain in Light 4 of 5: Arm the Lonely

   "Hello" by Shakespeare's Sister

Remain in Light 5 of 5: This Calamitous Life
   "Sunshine (Adaigo in G Minor)" by John Murphy
   "Nobody Loves Us" by Morrissey
   "Longest Day" by Soulsavers
   "No Cars Go" by Arcade Fire
   "Dreaming of You" by The Real Tuesday Weld

Little Victories

   "I Knew Prufrock Before He Got Famous" by Frank Turner

   "Goodnight Kiss" by Black Box Recorder

   "End Credits" by Laptop
Season Two

World, Shut Your Mouth Part 1: Towards Peace

   "A Question of Trust" by Their Hearts Were Full of Spring

   "Mr Blue Sky" by Electric Light Orchestra

   "Let's Get Started" by Frisbie
   "Let's Make This Precious" by Dexy's Midnight Runners
   "World, Shut Your Mouth" by Julian Cope

World, Shut Your Mouth Part 2: Words Hang in the Air

   "Words Hang in the Air" by The Ladybug Transistor

World, Shut Your Mouth Part 3: Predestination: A Beginner's Guide

   "Speedway" by Morrissey

   "Rise" by Public Image Ltd

   "Street Spirit (Fade Out)" by Radiohead

Twenty Plus One

   "Lost Property" by The Divine Comedy

   "S (Studio Version)" by Labradford

slaughterhouse

   "Dark" by Low

   "Dirge" by Death in Vegas

   "Waiting Rooms" by Simon Warner

    "Note to Self" by The Divine Comedy

slaughterhouse Part 2: The Road Not Taken

   "Teenage Spaceship" by Smog

   "Ladies and Gentlemen We Are Floating in Space" by Spiritualized 

   "Night and Day" by Pelvis

   "Pure" by The Lightning Seeds

Births, Deaths, and Interventions

   "The Devil, You + Me" by The Notwist

   "Don't You Forget" by Micah P. Hinson

   "Knowing The Ropes" by Michael Nyman

The Custom-Made Now - An Elegant Chaos Prologue

   "Blue Skies" by Longpigs

   "No Surprises" by Radiohead

Elegant Chaos Part 1: All Our Parlous Yesterdays

   "Fontanelle" by Clem Snide

   "An Elegant Chaos" by Julian Cope

Elegant Chaos Part 2: Stet

   "Where Damage Isn't Already Done" by The Radio Dept.

   "The Certainty of Chance" by The Divine Comedy

   "The Psychiatrist Is In" from God Help the Girl
   "A Europewide Search for Love" by Ballboy 

Elegant Chaos Part 3: Predestination: An Expert's Guide
   "It's the End of the World As We Know It (And I Feel Fine)" by R.E.M.
   "Good Goodnight" by Aqualung
   "If the World Ends" by Guillemots
   "Where Are They Now?" by Gene
The Permanent Revolution
   "The Village Green Preservation Society" by Kate Rusby
   "The S.A.S. And The Glam That Goes With It" by Earl Brutus
   "I Giorni" by Ludovico Eianudi
Our Steps Will Always Rhyme
   "Nobody's Empire" by Belle & Sebastian
   "Love Expression" by It's Jo And Danny
   "Hey, That's No Way to Say Goodbye" by Leonard Cohen
The Sensuous Frame
   "Last Night I Nearly Died (But I Woke Up Just In Time)" by Duke Special
   "Sweetest Decline" by Beth Orton
   "Cannonball" by The Breeders
   "Call Me Ishmael" by Get Cape. Wear Cape. Fly
   "Flightless Bird, American Mouth" by Iron & Wine
The Frail Gaze
   "She's Hearing Voices" by Bloc Part
   "The Light Pours Out Of Me" by Magazine
   "Velocity Girl" by Primal Scream
   "How Soon Is Now?" by The Smiths
   --used in-issue--
   "The Power of Love" by Huey Lewis and the News
   "What Presence?!" by Orange Juice
   "The Party Line" by Belle & Sebastian
   "Only Love Can Break Your Heart" by Saint Etienne
   "Let's Make This Precious" by Dexys Midnight Runners
The One Where They Go To Earth
   "I Love Pop Music" by Ben Lee
   Cheers theme tune
   "There Will Always Be" by Adem
The Not Knowing
   "Please, Please, Please, Let Me Get What I Want" by The Smiths
   "Song for the Leftovers" by A Camp
Some of My Best Friends Are Autobots
   "Loaded" by Primal Scream
   "Fool's Gold" by The Stone Roses
   "Shake Your Money" by Black Grape
Animals
   "It's Not Funny Anymore" by Babybird
   "Living With the Human Machines" by Strangelove
   "Bowl of Oranges" by Bright Eyes
The Lopsided Triangle
   "Wuthering Heights" by Kate Bush
   "Are You Ready To Be Heartbroken?" by Lloyd Cole
   "Water From the Same Source" by Rachel's

    "Avril 14th" by Aphex Twin
Speak, Memory: Part 1
   "Take Back The Days" by East River Pipe
   "You or Your Memory" by The Mountain Goats
Speak, Memory: Part 2
   "Monkey Vs. Shark" by Thee More Shallows
   "The Living Dead" by Suede
   "Losing My Religion" by R.E.M.
Silent Light (The Transformers Holiday Special)
   "It's the Most Wonderful Time of the Year" by Andy Williams
The Dying of the Light
   "Hurt" by Johnny Cash
   "Daydream In Blue" by I Monster [trailer theme]
The Dying of the Light Part 1: How Bright Their Frail Deeds
   "Heroes" by David Bowie
   "Our Life Is Not A Movie Or Maybe" by Okkervil River
   "Nonphenomneal Lineage" by Grandaddy
The Dying of the Light Part 2: The Sun in Flight
   "The Ship Song" by Nick Cave and the Bad Seeds
   "Foi Na Cruz" by Nick Cave and the Bad Seeds
   "The Sound of Silence" by Simon & Garfunkel
The Dying of the Light Part 3: Your Fierce Tears
   "Franklyn" by Michael Nyman
   "The Return of Evil Bill" by Clinic
   "Teardrop" by Massive Attack
   "Twilight of the Empire" by Farina
The Dying of the Light Part 4: At Close of Day
   "Make Your Move" by The Delgados
   "Little Things (That Keep Us Together)" by Scott Walker
   "Into Dust" by Mazzy Star
   "Out of Time" by Blur
The Dying of the Light Part 5: Rage, Rage
   "Slow Parade" by Broken Records
   "Superman" by Cinerama
   "The Birds Will Sing For Us" by Ed Harcourt
The Dying of the Light Part 6: Do Not Go Gentle
   "Here's Where the Story Ends" by The Sundays
   "Everything I Am Is Yours" by Villagers
   "Missing The War" by Ben Folds Fives
   "To The Rescue" by The Divine Comedy
Ten to Midnight
   "Rosemary Davis' World of Sound" by The Jazz Butcher Company
   "It's Not Alright" by Lambchop
   "Out To Get You" by James
Last Light
   "Who Said This Was the End?" by Gene
   "Casiotone for the Painfully Alone" by Bobby Malone
   "Something Like You" by Michael Head & The Strands
   "The Copper Top" by Bill Wells & Aidan Moffat
   "The Dogs And The Horses" by The Divine Comedy
Season Three

   "Graycoated Morning" by David and the Citizens
Dissolution
   "Neither Here Nor There" by Lost In The Trees
Dissolution Part 1: Some Other Cybertron
   "This Is Why We Fight" by The Decemberists
   "Magic In Here" by Go-Betweens
   "Water From The Same Source" by Rachel's
Dissolution Part 2: Anomie
   "It Ended On An Oily Stage" by British Sea Power
   "Optimo" by Liquid Liquid
   "Lille" by Lisa Hannigan
Dissolution Part 3: A World Misplaced
   "These Types of Songs" by Anthony Reynolds
   "A Stone" by Okkervil River
   "The Summer of Speed" by Andreas Mattsson
Dissolution Part 4: Bad Moon Rising
   "You" by Nils Frahm
   "The Bleeding Heart Show" by The New Pornographers
   "Next Exit (Stay)" by Interpol
Dissolution Part 5: Modes of Production
   "Just For a Second" by Orlando
   "Of Up and Coming" by Pedro the Lion
   "All of the Ants Left Paris" by Tarwater
Dissolution Part 6: This Machine Kills Fascists
   "Cloudy Shoes" by Damien Jurado
   "Everything You Paid For" by The Scotland Yard Gospel Choir
   "Favorite Color Blue" by Tom Brosseau
   "I Won't Share You" by Sixpence None The Richer
   "Black Sheep Boy" by Okkervil River
After Megatron (A Dissolution Epilogue)
   "Threnody" by Goldmund
   "Medicine" by Daughter
   "Without You" by Tobias Jesso Jr.
An Axe to Break the Ice
   "Mahal Kita" by Emmy the Great
   "Get Up" by The Blow
   "I Know a Place" by MUNA
   "Sad Stories" by Would-Be-Goods
Chasing the Infinite
   "Sleepy California" by Her Space Holiday
   "Who Do You Love?" by Mojave 3
   "Goethe's Letter to Vic Chesnutt" by Hefner
   "The Weakest Shade of Blue" by The Pernice Brothers
The Plotters' Club (Part 1): Full Circle
   "A Lack of Understanding" by The Vaccines
   "Yes" by McAlmont and Butler
   "Introducing Angels" by Destroyer
The Plotters' Club (Part 2): Filling in the Blanks
   "I Am The Resurrection" by The Stone Roses
   "Lost Myself" by Longpigs
   "You Can't Always Get What You Want" by The Rolling Stones
   "I'll Never Be Anybody's Hero" by Morrissey
The Plotters' Club (Part 3): Journey's End
   "Planet Sizes" by Steve Mason
   "Beat Surrender" by The Jam
Sardines
   "Your Silent Face" by New Order
    "Bored to Hear Your Heart Still Breaks" by Tullycraft
    "Good Fruit" by Hefner
The Ties That Bind
   "Time For You" by Speedy
   "Adios Amigo" by Michael Head and the Red Elastic Band
   "Let It Roll" by The Silent League
Kill All 'Cons
   n/a
The Everlasting Voices
   "Twilight" by Electric Light Orchestra
The Everlasting Voices (1): Metastasis
   "Let Me Live" by Queen
   "Kelly Watches the Stars" by Air
   "Perfect Day" by Lou Reed
   "Jesus, Etc." by Wilco
The Everlasting Voices (2): The God War
   "I'm Ready to Move On/Wild Heart Reprise" by Bleachers
   "All Your Secrets" by Yo La Tengo
   "Your Belgian Things" by The Mountain Goats
   "Waitin' For a Superman" by The Flaming Lips
The Everlasting Voices (3): You Are Here
   "Wanting What I Can't Have" by Carla J. Easton
   "Water" by Ra Ra Riot & Rostam
   "Foreverland" by The Divine Comedy
Crucible
   "The Shepherd's Boy (Breaking the Wall)" by Murray Gold (Doctor Who Series 9)
Crucible (Part 1): A Dance Before Dying
Crucible (Part 2): Lustrare
Crucible (Part 3): Farsickness
   "The Scientist" by Coldplay
   "Sons and Daughters" by The Decemberists
Crucible (Part 4): The Return of the King
   "Cassandra" by Emmy the Great
Crucible (Part 5): The Unremembering
Crucible (Part 6): A Spark Among Embers
   "The Shepherd's Boy (Breaking the Wall)" by Murray Gold (Doctor Who Series 9)

Unsorted

   "Small World" by Roddy Frame

   "Wild Roses" by Bill Ryder-Jones
How to Say Goodbye and Mean It: Part 2
   "Human" by The Killers
   "Here It Comes (The Road) Let's Go" by Spiritualized
   "Go West" by Pet Shop Boys
   "Let's Get Out of this Country" by Camera Obscura
   "Lost Light" by Retronym
Character themes

   Brainstorm-- "Left To My Own Devices" by Pet Shop Boys
   Chromedome & Rewind-- "I Would Fix You" by Kenickie
   Cyclonus-- "Chicago" by Sufjan Stevens
   Getaway-- "I Spy" by Pulp
   Megatron-- "The Old Man's Back Again" by Scott Walker; "Speedway" by Morrissey
   Nautica-- "Fiction" by The Lucksmiths

   Rodimus-- "I've Got a Plan" by My Friend the Chocolate Cake
   Rung -- "Still Fighting It" by Ben Folds
   The Scavengers-- "Meaningless" by The Ballet

   Skids-- "Nobody Does It Better" by Carly Simon
   Tailgate-- "Hello Cruel World" by Mark Oliver Everett
   Ultra Magnus-- "True Men" by John DeRosa
   Whirl-- "Getting Away With It (All Messed Up)" by James

Spotlight

Omega's Conundrum 

   "Soft Light" by Frausdots

The Reluctant Specialist 

   "No One Said This Would Be Easy" by Cloud Cult

   "Only Living Boy in New Cross" by Carter USM

The Waiting Game
   "Enjoy Your Worries, You May Never Have Them Again" by The Books

   "The Distance" by Cake

John Barber

Robots in Disguise / The Transformers

Dark Cybertron

   "Trash City" by Transvision Vamp

   "Full of Fire" by The Knife

   "San Francisco" by Foxygen

   "Objet Petit A" by Harouki Zombi

   "We Do Parties" by Deerhoof

   "Siren" by Arrington de Dionyso and the Old Time Relijun

   "Black Skinhead" by Kanye West

   "Reflektor" by Arcade Fire

All Hail Optimus Part 6: No Fair Fights

   "Chimes Broken" by Holy F***

   "Stomach It" by Olga Bell

   "No Fair Fights" by Prick

Optimus Prime

Starscream: The Movie
   "Danger Zone" by Kenny Loggins
   "We Don't Need Another Hero" by Tina Turner
   "Rainbow Connection" by Kermit the Frog
   "Gloria" by Laura Branigan
   "I'm Alright" by Kenny Loggins
The Falling, Chapter 1: Surfeit of Prime

   "The Supermen" by David Bowie

   "No Church In the Wild" by Jay-Z and Kanye West

   "Ascendant" by Keep of Kalessin [song choice actually from artist Kei Zama]
The Falling, Chapter 2: Another Mine
   "Solitude Standing" by Suzanne Vega

   "Adore" by Savages
The Falling, Chapter 3: The Ground
   "Repo Man" by Charlotte Hatherley
   "Amplivagent" by T.A.R.
The Falling, Interlude: The First Who Was Named
   "Blackstar" by David Bowie
   "Killing Game" by Skinny Puppy
The Falling, Chapter 4: The Hallowing
   "Controller" by Hercules & Love Affair
   "Strangers" by St. Vincent
The Falling, Chapter 5: Endless Forever
   "Never Land" by The Sisters of Mercy
   "A Means to an End" by Joy Division
The Falling, Chapter 6: Unforgivable

   "The Big Decision" by Gail Ann Dorsey
   "Cygnet Committee" by David Bowie

Nick Roche

Last Stand of the Wreckers

   "Percussion Gun" by White Rabbits

Sins of the Wreckers

Issue 1

   "Bliss" by Tori Almos

   "A Forest" by Bat For Lashes

   "Last Of Our Kind" by The Darkness
Issue 2
   "Nature Trails" by The Comsat Angels
   "Hunter" by Bjork
   "Trimm Trabb" by Blur
Issue 3
   "Lovesong" by The Cure
   "We Used To Be Friends" by The Dandy Warhols
   "Lullaby" by The Cure
Issue 4
   "Waters of Nazereth" by Justice
   "No Distance Left To Run" by Blur
   "The Last Supper" from 1996 Jesus Christ Superstar Cast Recording
Issue 5

   "Kooks" by David Bowie

   "Optimistic" by Radiohead

   "Face the Day" by The Negative Way

   "Wall of Death" by Richard Thompson