I personally haven't seen most of those movies, the only ones I did see are the Aqua teen Hunger Force movie, Simpsons movie, Ratatouille, and TMNT. To be perfectly honest the movies I think SHOULD be in the stupid ass small 3 available slots are Ratatouille, TMNT, and Beowulf.
Now I have not seen Beowulf nor do I plan to but from what I see the movie looks like a visual feast of kick ass animations, and I trust Zemeckis seeing as how he is a kick ass director. I believe Ratatouille and Shrek the 3rd have the best chances of winning (despite I've heard Shrek was craptacularly bad).
I thought TMNT was fantastic and I hope that makes it in the top 3, I felt that was such a better constructed movie in story, characters, and voice acting. Surfs up looked completely stupid if you asked me. It looked like an unintelligent mess of cheap, uninteresting characters and a plot that sounds superbly lame.
However, even though I'm pretty positive Aqua teen will not even be in the top 3, if it does, I will laugh my ass off uncontrollably because if anyone has seen that movie its hilarious to think a movie with THAT kind of content is in nominational status with the likes of Pixar and such

.