I'd go
Toy Story - Classic, iconic, CINECAST!ing awesome. A real wowzer and a screenwriting 101 example of how to tie the narrative together in perfect unity.
Monsters Inc. - Visual mastery. Pure fun.
A Bug's Life - Punctuates the theme in a powerful way. The climax is a mixture of hope and fear. It also gives one of the most powerful villains of Pixar's a brutal yet foreshadowed comeuppance.
Toy Story 2 - Extremely satisfactory. "Well, let's find out!" Epic, I shed a tear. A precursor to Monsters Inc. with the conveyor belts, but it's ultimately better executed there than here.
Ratatouille - A truly WTF, is this really happening? collection of scenes. Hilarious too, but the ending is far more memorable for what comes before and what comes after.
The Incredibles - It's a big battle, well-edited, not much different than most big superhero battles, but fun.
Cars - Again, much like The Incredibles, it's fine, "the big race", everything ties together nicely, it's funny, but it's just not as memorable, satisfying, or unique as my top 4. I also feel that the flashbacks feel a little forced here.
Toy Story 3 - Lightly manipulative? Forcing a iconography? Ehhhh, I am quite mixed about this ending, even though I have to give Pixar credit for going there.
Finding Nemo - It begins well, but I ultimately dislike this climax. It's mostly the Net scene. It just kind of comes out nowhere? It doesn't hearken back to much that happened in the actual plot, it's more like, "I learned my lesson and here is how I implement it!" Yuck.
Wall-E - I had to read 1SO's chapter review to even remember this scene. A lot of fat people roll over and Wall-E may die (but he won't, Pixar starts on its roll of "lets fake-out the audience by almost killing the protagonist" cliche).
Up - Uhhhhh, two old men fight and some stuff happens. Completely forgettable.