1. Monsters Inc. - I'm biased towards what's more emotionally involving to me, and this is the one I found the most moving because of the relationship between Sully and Boo. And it had a perfect balance of sentimentality and great comedy too because Billy Crystal was so funny in it.
2. Toy Story 2 - An improvement of Toy Story, which is an amazing accomplishment in and of itself since I thought Toy Story was pretty much perfect.
3. Toy Story
4. A Bug's Life
That's about all I've liked from Pixar. I don't know if it's just because I turned 20 at the time, but "Finding Nemo" was the point when I stopped caring. In "Finding Nemo", "The Incredibles", and "Ratatouille" I just started caring less and less about the characters and finding the stories less and less interesting.
I thought all the characters in "Finding Nemo" were annoying, and I was shocked when everyone said "The Incredibles" was great for adults and kids because all I saw when I watched that movie was way too many action/chase/fighting sequences and not nearly as much heart as the early Pixar movies or even Brad Bird's own "The Iron Giant".
The animated action sequences didn't impress me, because I knew I was just watching characters made on a computer. I know they were a family who supposedly loved each other, but that didn't come through to me. As for "Ratatouille", well...I just couldn't bring myself to care about a rat, no matter how sweet they tried to make him.
I haven't seen any Pixar movies since those three (and I skipped "Cars") as I liked each one less than the one before from 2003, and they each made me less interested in Pixar movies. They got me doubting that I'll ever be able to enjoy a Pixar movie again, but the rave reviews "Up" is getting tempts me to give them another chance.