Edit: Added some items. To see who suggested what, scroll down to the comments. I also put the list under a cut as it's getting a bit long.
By Optimus Prime
1. Back to the Future
Why: Perceptor and Wheeljack built a time machine.
2. Cartoon Network
3. This is Spinal Tap
Why: See incident report. Incident number 9.
4. Discovery Channel
Why: Removed from list due to Perceptor's glare of angry kitten doom.
Why: Perceptor and Wheeljack.
6. Bill Nye the Science Guy
Why: See number 5.
7. Jurassic Park
Why: Ratchet and Wheeljack. Too late.
9. The Song That Never Ends
Why: Blaster. Song added at the request of Eject and Rewind.
10. Willy Wonka and the Chocolate Factory
Why: Red Alert. Show added at Inferno's request.
12. Silent Hill
Why: Unknown. Movie added at Perceptor's request. Removed from list at the request of a rather creepy little girl. How the hell did she get on the Ark anyways?
13. Land Before Time
Why: See number 8.
14. Home Alone
15. Lord of the Rings
Why: Dinobots. Added at the request of Mirage. Also added at the request of Ratchet. Note to Ratchet: Did they really stand in front of Devastator and shout "YOU SHALL NOT PASS!"?
16. Peter Pan
17. Harry Potter
18. History Channel
Why: Unknown. Requested by Spike and Sparkplug.
Why: See number 9. Video has also caused numerous fights.
Why: Requested by Bumblebee and Bluestreak.
21. Speed Racer - All Versions
Why: Twins, Tracks, and Blurr. Especially Blurr.
22. House, MD
Why: Ratchet. He's bad enough as he is, no need to give him any ideas.
24. Ripley's Believe It Or Not
Why: Ratchet, Wheeljack, Perceptor, Skyfire. Something about foam. Don't ask.
25. Star Wars
Why: Unicron. Note to Autobots: Unicron is not the Death Star, no matter how much you think he looks like it. Note to Red Alert: No, the humans are not in league with the Chaos Bringer. Please put the cannon down now.
26. Children's Songs
Why: See number 9.
27. The For Dummies book series
28. The Complete Idiot's Guide [entire series]
Why: See number 27.
29. Military Channel
Why: Warpath. Added at the request of the United States Armed Forces.
30. Paranormal Television Shows
Why: See number 11.
Why: The song I Kissed A Girl. Note to Blaster and Jazz: Blasting that song, repeatedly, at high volume will not get me to remove MTV from the list.
32. I Kissed A Girl
Why: Blaster and Jazz.
33. Dark Cloud
34. Book: Animal Wise, the Spirit Language and Signs of Nature
Why: Hound and Beachcomber. Note to Hound and Beachcomber: No, we do not care what it means when animals look at us and fluff their fur a certain way. Shut up about it already.
35. Antique Roadshow
36. Breaking Vegas
Why: See number 35.
37. Health Channel (only allowed in previously approved areas)
Why: Causes ill health. Requested by everyone not in a medical profession.
38. Books on Etiquette
39. Metal Gear Solid
Why: Mirage. Something about boxes.
40. Handyman Books
Why: Wheeljack. Let's keep the inventions in the lab, please.
Why: "Believe it!"
42. Voodoo Dolls
Why: Trust me, you don't want to know.
43. Shrunken Heads
Why: See number 42.
42. Power Rangers (All Versions)
43. Reading Rainbow
Why: Perceptor and Bluestreak.
44. The Making of the Dictionary
Why: Perceptor. This show must be kept from Perceptor at all costs.
45. Artemis Fowl
Why: Red Alert, Wheeljack, and Perceptor. Note: No, Red Alert, there are no faeries under the floor. Wheeljack, don't even think it. And Perceptor, put that down!
46. Monty Python
Why: The Twins, Wheeljack, and Perceptor. Something about bridges, killer rabbits, and swallows. I really don't want to know any more than that.
47. It's A Small World After All
Why: Twins. Added at the request of everyone (including Blaster, much to my surprise. Apparently, there are songs he doesn't like).
Why: Perceptor. Something about L-Space (whatever that is), Dungeons, and... the Rite of AshkEnte? Added at the request of a robed skeleton (I'm not even going to ask).
Why: Perceptor. Note to Perceptor: I don't care how cute you think it is; you are not keeping it!
50. Forensic Files
Why: Red Alert. He really doesn't need anymore ideas.
51. Murder By the Book
Why: See number 50.
Why: Again, see number 50. Whose bright idea was it to let Red Alert control the remote anyways?
Why: Have you seen the things on Youtube? *shudders*
Why: Added at the request of Smokescreen and Ratchet as they claim it has traumatizing effects.
55. Demolition Derbies
Why: Counselling costs too much (though Smokescreen wasn't complaining).
Why: Requested by Blaster. Note to Crew: No, the Cassettes are not Pokemon and you do not need to catch them all.
Why: Red Alert, Wheeljack, and Perceptor. Red Alert is paranoid enough, and Wheeljack and Perceptor have already caused more than enough damage.
58. First Person Shooter Games
Why: Prowl, who somehow figured out how to program the targets to look like the twins and Jazz.. Note to twins and Jazz: Please leave Prowl alone when he is in that kind of mood.