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.