Here's my breakdown (disclaimer: this list has been known to fluctuate at a moment's notice and I reserve the right to change my mind on this later on):
1) I would have to go with Ratatouille on this one. An absolutely beautiful film with a fantastic heart, wonderful writing, great performances, and, of course, the incredible Brad Bird at the helm.
2) The first act of WALL•E is, in my humble opinion, the single most perfect piece of film ever to grace cinemas. The second and third acts may not be quite as astounding, but they're still nothing short of excellent and showcase all the wonderful things we've come to expect from Pixar: deep characters, beautiful visuals, heartfelt emotions, etc. etc.
3) I know I'm in the minority here, but I think Toy Story 2 is the best of the Toy Story films and an absolutely perfect template by which all other sequels should be judged. "When She Loved Me" is still the most poignant Pixar moment to date for me, and that is quite an accomplishment.
4) Up is an absolutely wonderful film from start to finish, it's simultaneously a grand adventure film and an intimate human drama. It handles themes that most producers of "kids movies" would balk at, yet handles them in a way unrivaled by even its live action contemporaries. I still think it's criminal that this one didn't take Best Picture in 2009.
5) While I may prefer Toy Story 2, Toy Story 3 is an incredible achievement all on its own. Toy Story 2 had a really fantastic ending with a strong sense of closure and having a second sequel was entirely unnecessary, but Lee Unkrich completely justified Toy Story 3's necessity by allowing the same amount of time that passed in the real world to pass in the world of the film. As a kid who grew up at roughly the same pace as Andy the film made a special connection with me and I feel retroactively improved the first two. It brilliantly wraps up the stories of these characters and ends the series in a way that few other final films have ever managed to do.
6) Andrew Stanton's first feature directing, Finding Nemo, is probably the most visually beautiful film this side of WALL•E (also an Andrew Stanton pic) that Pixar has ever done, but it doesn't settle for just being gorgeous, it also has fantastic characters and a deeply moving story. While Toy Story may have put Pixar on the map, I would call Finding Nemo the film that solidified their reputation. Not only was it their fifth film in a row to be a major hit with both critics and audiences, it also shattered box-office records, and is still one of the highest selling DVDs of all time.
7) Even with all the Super Hero films that have come out over the last decade or so, The Incredibles could easily sit on a list of the Top 5 alongside the likes of The Dark Knight, Spider-Man 2, Superman: The Movie, and Marvel's The Avengers. I still hope that Bird will make his way back to Pixar one of these days to direct a sequel, because of all the Pixar properties, this one is the most deserving of a follow-up.
8) You know, a lot of people tend to forget A Bug's Life and I've never been quite sure why. It's a wonderful and highly ambitious film with a great cast of characters, beautiful visuals, and one of the most exciting final acts Pixar has ever done. I still get chills during the scene where Flik stands up to Hopper.
9) Monsters, Inc. is one of those movies that can barely contain it's creativity, and while I'm looking forward to getting to see Cars Land, and I love the theming, if not necessarily all the attractions of a bug's land, if there was ever a Pixar film that deserved a theme park land it's this one. Unfortunatley the only MI attractions we have on this side of the Pacific are decent, but don't even come close to taking full advantage of their source material.
10) Brave is a very good film that doesn't try to do anything groundbreaking or unique, but instead takes an age old story and formula and spins it in a way that only Pixar could. It's the best Disney Fairy Tale I've seen in a long long time.
11) Now I'm going to get flack for putting Toy Story so low on this list, but keep in mind that all the movies thus far on this list are so far ahead of what most other films are doing in Hollywood that despite being this low on the list it is an absolutely incredible film. The reason Toy Story is all the way down here is simply because, while it's a great movie, I think Pixar has improved leaps and bounds from where they started in 1995 (even though they started so far ahead of everyone else to begin with). Toy Story may be Pixar's most important film, but I don't think it's their best.
12)While some might call Cars Pixar's first mis-step, I personally think it's a very good film that just isn't quite as good as any of the other films in Pixar's library of hits. It features all the staples that Pixar is known for: compelling characters, great visuals, honest emotions, etc. and with rare exceptions like the brilliant How to Train Your Dragon and the charming Winnie the Pooh, it's still better than anything rival animation studios are putting out.
13) Cars 2, however, is a true mis-step for Pixar. While Pixar is known for stunning visuals, great characters, and stories filled with a strong heart and honest emotions,Cars 2 opts to go the route of a mediocre action-comedy with forced sentimentality that comes across completely hollow and makes the mistake of upgrading Mater (who worked as a supporting comic-relief character because he was fairly one-note) to the leading role. It's not a terrible movie by any means, or even really a bad one, but it's very mediocre and that's a major disappointment coming from Pixar.