My favorites:
10. Batman Beyond: The Return of the Joker (it's a BTAS spinoff, so I guess it's comic-based)
9. Spider-Man
8. Spider-Man 2
7. The Incredible Hulk
6. Batman (1966)
5. The Dark Knight
4. Turtles Forever (I'm really disappointed this hasn't had an uncut DVD release)
3. Teenage Mutant Ninja Turtles
2. Batman: Mask of the Phantasm
1. Superman
Hardware gets an honorable mention (I don't know if it can officially be called a movie that's based on a comic), as does Howard the Duck (I liked it as a kid, and I love the original comics) and Conan the Barbarian (I was first introduced to Conan through Marvel's Conan the Barbarian and The Savage Sword of Conan).
The Tim Burton Batman films would be on the list if Batman didn't kill so many of his enemies without a second thought.
And Captain America: The First Avenger would likely be on the list, if I'd seen if yet. I'm waiting 'til the night before I see The Avengers to watch it (I've really liked all of The Avengers "prequels," especially The Incredible Hulk, and I expect The Avengers to be a new favorite). =)