I voted for Ratatouille. Just an original, well-made movie that had me guessing at every turn. Plus, I’m a sucker for stuff like Ego’s review at the end of the movie.
My 2 year old son votes for Cars.
The ones I’ve seen are, in order of release from newest to oldest:
Up - I loved the opening montage, also liked the symbolism of the old man carrying his house around, but as a film I don’t see it as very strong. It did feel out of place that the villain had to die at the end.
Wall-E - Should have been called iRobot. Didn’t like it too much, felt the character design of Wall-E was so manipulative. They might just as well have used a sad puppy.
Ratatouille - I have a big issue with how Colette goes from strong and independent to soft and attached to Linguini.
The Incredibles - Liked it a lot. It did borrow a bit too much from Fantastic Four, but it made up for it with good locations and pacing.
Monsters, Inc. - It didn’t click with me.
Toy Story - Not bad, I like it. It’s not as dated as one might think, either.
I would agree that Pixar movies generally have better first than second halves. Well-E and Monsters, Inc are prime examples of this for me. Wall-E in particular would have worked best as short film, the Wall-E character is very similar to The Lamp.
I’d be torn between UP and The Incredibles. The Incredibles obviously because it’s just great start-to-finish. UP deserves a lot of credit for pushing the boundaries of what Pixar produces, and has a more interesting message than any of their other output (or in fact most of Hollywoods output). The fact they use this message as the basis for an otherwise fun family film is remarkeable IMO. It certainly brought a tear to my eye.
Although The Incredibles got my enthusiastic vote, I did enjoy Up. My boys and I will still exclaim “Squirrel!” when we see one. 
I’m in this small minority with you. I’m both a NASCAR fan and a Route 66 enthusiast, so I was probably predisposed to enjoy it more than most people anyway. But I still think it holds up on its own merits. It was just huge fun from start to finish. I loved it.
Never saw a Pixar film I didn’t enjoy to some extent, though…
The Incredibles is probably one of the best James Bond movies ever, even though it doesn’t have James Bond. It got my vote…Finding Nemo a close second.
(the “where is my super-suit??!?” scene with FroZone makes me laugh just remembering the dialog.)
1st half of Wall-E may have been pure genius. Got a little tiresome once they get on the ship.
Dug’s squirrel joke from Up is, I think, the hardest I’ve laughed at a movie in 10 years. Yes, that includes The Hangover and everything by Judd Apatow.
Sid to me is the difference that makes Toy Story the best: the best villain. Genuine terror being a toy stuck in his lair. And lotsa funny quips and references.
Finding Nemo a close 2nd. Great hero’s journey and sweetly emotional.
This is going to be a minority view, but my favorite Pixar film is the short “Boundin’”.
The love it’s getting in this thread finally prompted me to see Finding Nemo, and while I thought it was good, I’d still rate it well below most other Pixar movies. I’m guessing it would have resonated much more with me if I had kids… How many people who rated it as best are parents?
I didn’t rate it best, but it’s up in my top 3. And while I’m not a parent, I’m someone whose mom shared many of Marlin’s overprotective fears (due to the death of my brother) and who imparted some of those fears to me. So Marlin’s terror of losing his family really hit home for me, as did Dory’s sweet, touching memory issues and the desperate attempt to avoid losing Marlin’s friendship/being alone. The fact that the film is freakin’ gorgeous didn’t hurt either.
Maybe you’re just not neurotic enough, Chronos. 
I’m not a parent, but I loved Dory’s character, for the touching moments and the funny ones. (“I wish I could speak whale.”) And yes, it was a very nice film to look at. While I pit it a notch below #1, it was above Pixar’s average for me.
Saw Toy Story 3 last night, it is going to be high on a lot of people’s lists.
I am jealous! Toy Story 3 is getting early rave reviews–I can’t wait to see it!
I voted for “WALL-E,” but it seems unfair to NOT vote for masterpeices like “The Incredibles,” “Finding Nemo” and “Toy Story” (either one.) Even their not-so-great films are very good.
They’re among the best films made in the last 15 years, animated or not.
“Ooo, look, krill!”