My order would be as follows....
1.) Toy Story 3 - One of the few movies to make me openly weep in theaters. I cry at movies a lot, but can usually contain myself in public. This one just broke me. Beautiful movie.
2.) The Incredibles - Up there in terms of best super hero movies period.
3.) Finding Nemo - Wonderful story, beautiful movie, funny, charming, masterpiece.
4.) Up - The first ten minutes of this movie are pure perfection. Emotionally heart-wrenching, you'd have to be a monster not to get a bad case of the feels with this. Rest of the movie never reaches that level, but is still fantastic.
5.) Wall-E - Can't quite put my finger on why I like this one so much, second half has some major issues, but the first half with Wall-E on a desolate Earth is chilling and mesmerizing.
6.) Brave - I thought for their first attempt with a female lead Brave was incredible. Loved Merida, her story may have connected with me on a deeper level personally, and that maaaay be clouding my judgement. But that movie had great action, pulled at the heartstrings, great music. Awesome.
7.) Ratatouille - Hilarious, not much more to say. Maybe the most flat-out charming movie on this list.
8.) Toy Story 2 - Yeah, I like it better than the first one, not by much, but people still think I'm crazy for that. Lot of great humor though, touching story about being forgotten and beginning to drift out of childhood.
9.) Toy Story - I mean, it's Toy Story, it's down on this list only by necessity, this is probably the Pixar movie that's closest to my heart, definitely seen it the most. Wore out two VHS copies when I was a kid.
10.) Monsters Inc - I like the world, I like a lot about this movie. Nothing ever hits "love" levels though. Good stuff, but not near my favorite.
11.) Monsters University - See above, like its predecessor still really good, but hard to keep up with this company.
12.) A Bugs Life - I liked A Bugs Life as a kid, but it doesn't hold up. Still has some really funny bits, but flat story, not a whole lot going for it.
13.) Cars - I like the idea, and the French car.
14.) Cars 2 - Ugh.
Looking at it now, the bottom two are the only ones that I never enjoyed at any point in my life. A Bugs Life is pretty meh, but other than that, man Pixar has a GREAT track record.