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This list is not in any particular order.

1. Change all the actors into CG
   by AJ of the Sith

2. Count Dooku points out to the Geonosians that the schematic for their secret weapon shows an unshielded thermal exhaust port that could cause some problems.
   by Davidw

3. All the boring parts cut out (making this the 1st Special Edition to be less than half the running time of the theatrical release)
   by Davidw

4. Zam Wesell shoots at Obi-Wan Kenobi before he chops off her arm.
   by Tycho Celchuuu

5. Anakin/Padme love subplot replaced by shots of ewoks and gungans dancing to non-John Williams music.
   by Tycho Celchuuu

6. Jango Fett hits his head on another 6 doors, in case just one was too subtle.
   by Tycho Celchuuu

7. Opening crawl font changed to "Stencil," because it looks really cool.
   by Tycho Celchuuu

8. Jedi now drink Pepsi, and the evil Count Dooku receives funding from Coca Cola.
   by Tycho Celchuuu

9. 90% more clones!
   by Darth Rob

10. Real-time lighting effects for Obi-Wan's beard.
    by Rin, Destroyer of Keyboards

11. Anakin will exclaim "Yippee" after kissing Padme for "continuity's sake". Then again, wouldn't many of us?
    by Wild Karrde

12. Laugh track added to fireplace love scene.
    by Cirrocco

13. The movie now starts when Padme and Anakin are in the droid factory.
    by The Trickster Fox

14. The Jango Fett clones get replaced by Smith clones (who survive longer and can actually shoot AND kill ppl!)
    by The Trickster Fox

15. More hidden cameos then you can shake a (death)stick at!
    by The Trickster Fox

16. Yoda will parade around in a santa costume in order to promote the new figure.
    by Darth Nima

17. Lucas: When Jango Fett loses his head he does a dance!
    by Kar'Ghun

18. Well first they'll change the title, then replace Dorm? in the opening scene with Jar-Jar Binks...
    by Darth Nima

19. Using new and improved CGI technology, Lucas will now add Chemistry to Anakin/Padme scenes.
    by BlackWolf

20. Ten-minute scene where an alien babe tries to hit on Anakin in the bar on Coruscant.
    by Keith

21. All of Obi-Wan's fight scenes are re-done as musical numbers from Moulin Rouge!
    by Serinthia Draftwood

22. Count Dooku unleashes the power of the One Ring on Yoda
    by empirestrikes

23. Remember that bikini leia wore in Return of the Jedi? Guess what Padme is wearing...
    by Zedium

24. The Shaft theme plays during the brief fight between Mace Windu and Jango Fett.
    by Darth Hideous

25. A special CG tap dancing Jawa at Anakin and Amidala's wedding.
    by BrenDarklighter

26. Anakin's Extended Sand Monologue
    by DoogieTheHutt

27. In a surprise vote, Palpatine is recalled from the Senate and replaced with Arnold Schwarzenegger
    by Obi No

28. A hot love scene between Anakin and Padme, ala Matrix Reloaded, since that scene was SOOOO effective...
    by Warlord Tarkov

29. They'll put a band number in the club on Coruscant.
    by Ruroumi Jedi

30. When Jango loses his head, it bounces against a door frame.
    by Rin, Destroyer of Keyboards

31. All references to fighting, weapons, and war have been edited out.
    by Rin, Destroyer of Keyboards

32. The entire movie animated into the style of that new Clone Wars cartoon coming to the Cartoon Network.
    by Dan Reyes

33. The war begins on Hoth, and Yoda shows up in Dooku's hangar wearing his Santa outfit.
    by Long-Gon Jinn

34. When Anakin jumps out of the speeder in Coruscant, we hear a drawn-out "YYYYYYYIIIIIIIIPPPPPPPEEEEEEE!"
    by Long-Gon Jinn

35. head falls out of Jango's helmet.
    by Vesp

36. the anakin nightmare scene is dubbed over "padme, padme" instead of "no, no"
    by Bant Eerin

37. In the bar on Coruscant, Anakin stops and talks about how sand is course and rough with a table full of hot alien women.
    by Darth Seminarian

38. Padme hits that red button a third time with yet another result.
    by Mr. Whitmarsh

39. a shocking scene involving a real set.
    by nerdus

40. Jabba the Hutt will be digitally replaced with a fat Scotsman
    by Jenk

41. Obi-Wan and Anakin dancing on a table and singing "ho ho to Naboo I go"
    by Ember Stryder

42. The opposite of the original trilogy SE!!! All CGI replaced with Live action
    by darth_guy

43. Half of the Clone army is wiped out when they realize they are the original stormtroopers, and can't hit the broadside of a Trade Federation drop ship.......
    by Jesphobo

44. All the lame deleted scenes put back in, all the cool deleted scenes left out.
    by Rin, Destroyer of Keyboards

45. Which special edition do you mean? The VHS special edition, DVD special edition, re-release to theaters special edition, IMAX special edition, Holiday special edition, or Jar Jar's Big Adventure special edition?
    by Darth Lairdman

46. They're going to change the Special Edition of "Attack of the Clones"!? Why was I not told about this Special Edition?
    by Darth Nima