Please bear in mind, this is all relative. Pixar has made so many great pictures that even the ones in the bottom third are still great fun. In my opinion, Pixar still hasn't made a bad movie - no, not even Cars 2.
1) Toy Story 2: Among computer animated films, the emotional pinnacle is still "When She Loved Me." Pure and simple.
2) Wall-E: I vividly remember seeing this movie for the first time and calling up at least three friends telling them to go see it immediately. Besides, how many sci-fi movies have the guts to open with a tune from Hello Dolly?
3) Up: Movies aren't supposed to make you cry within the first 10 minutes, dammit.
4) Toy Story 3: Whereas Up was Pixar's best beginning, this movie had the best ending.
5) The Incredibles: Still my favorite superhero movie of any kind, live action or otherwise. Yes, it's even better than The Avengers.
6) Monsters Inc.: The Chaplin-esque final shot is eloquently perfect.
7) Toy Story: I see this one often listed as Pixar's best. It's not, wonderful as it is. It is indisputably a landmark film, but both sequels are superior. How many other film series can say that?
8) Ratatouille: No, that final statement about critics didn't resonate with me at all. Nopity, nopity noooo. (sarcasm)
9) Finding Nemo: A lot of people would name this as their favorite non-Toy Story Pixar movie. I didn't fall as much in love with it as everyone else, but it was certainly Pixar's most beautiful movie - until very recently, anyway.
10) A Bug's Life: This one tends to be forgotten among Pixar's output, and wrongly so. It's not transcendent, certainy, but it's wonderfully entertaining in the way it juggles multiple characters, Seven Samurai-style.
11) Cars: For the first time I got the feeling that Pixar let other considerations (like selling soundtracks) get in the way of the story, but its lamentation of a bygone era (Route 66, etc.) is still deeply affecting, especially for someone like me who revered the Beatles when his peers were listening to Ratt.
12) Brave: I saw the movie a second time, and while it played better for me than it did the first time, I still felt jarred by the shifts in tone, which might be attributable to the fact that directors changed midstream. All that said, I think a lot of critics missed the boat by undervaluing this one. I agree with this astute observation: " If you're expecting something as deep as the first ten minutes of "Up" or the last ten minutes of "Toy Story 3," you're not going to get it. "Brave" isn't aiming for the same emotional targets; its focus is more childlike, as opposed to profound and slightly wistful. If you try to compare "Brave" to the collective weight of something it's not, rather than judging it on its own terms, you're going to be disappointed."
13) Cars 2: I will grant you that Pixar was coasting with this one, but I will not grant you that it's a misfire. It was still a very fun coast. This longtime James Bond fan loved all the homages to spy movies, and even though I am not a car aficionado, I still loved the idea that lemons were the villains. This movie was NOT itself a lemon.