It's been mentioned in a few other similar threads, but here are the attractions they don't want you videotaping in:
Magic Kingdom
1. Monsters Inc. Laugh Floor (my guess is because it involves audience members)
2. Stitch's Great Escape! (not sure why exactly, other than the harness makes it more difficult to hold the camera)
3. Carousel of Progress (absolutely no clue why)
Epcot
1. Honey, I Shrunk the Audience (probably because of the actors in it; I'd say it's because of the 3-D, but they don't care if you tape Philharmagic or Muppet-Vision)
2. Soarin' (most likely because you're suspended so high off the ground. Drop a camera and kiss it goodbye)
3. Ellen's Energy Adventure (again I'm guessing a case of the actors)
4. Cranium Command (when it's open; another case of many actors)
5. Body Wars (when it's open; also hit or miss. Sometimes they don't care, other times they do)
6. The Making of Me (when it's open; not sure why since Martin Short is okay with people taping O' Canada!)
7. The American Adventure (no idea)
8. Impressions De France (again, no idea)
Disney-MGM/Disney's Hollywood Studios
1. Sounds Dangerous (because of the actors in it, maybe?)
2. Star Tours (no freakin' idea. You can tape it all you want at Disneyland, so this making zero sense. Then again, you can tape Muppet-Vision here, but not at California Adventure. Go figure...)
3. One Man's Dream (the movie part, no idea why. They wouldn't let you tape it when Michael Eisner narrated it, so I don't think it's Julie Andrews requesting it)
4. Rock n' Rollercoaster (I'd say Aerosmith, or that they don't want you dropping your camera in the middle of one of the loops)
5. Tower of Terror (Similar to RNRC, they're probably afraid someone will let the camera go during a drop and it will smack someone on the head on the way back up)
Animal Kingdom
1. It's Tough to be a Bug (the actors, I'm guessing)
2. Dinosaur (I've only encountered this once, but you never know. I had a CM on Spaceship Earth tell me no recording once, too)
I think that's all of them. If I remember another, I'll post it.