Haven't seen TS3, haven't seen Cars.

1. Ratatouille
2. Toy Story 2
3. Wall-e
4. The Incredibles
5. Toy Story
6. A Bug's Life
7. Finding Nemo
8. Up
9. Monsters, Inc

EDIT: Added Bug's Life

1. Monsters, Inc.

2. Toy Story 3

3. The Incredibles

4. Wall-E

5. Finding Nemo

6. Toy Story

7. Toy Story
 2
8. Cars

9. Bug's Life

10. Ratatouille
11. Up

1.  The Incredibles

Then,  literally in no particular order because I can't choose among them and you can't make me.

Ratatouille   Monsters Inc.  Finding Nemo

Next, only slightly less awesome, on an awesomeness scale that is still entirely awesome:

Wall-E, Toy Story, Up

Near the end, only because it's been so long since I've seen them that I don't remember them.    I'm sure if I watched either of them right now I would love them.

Toy Story 2, Bug's Life.   

10th  because I haven't seen it yet:

Toy Story 3

11.  Cars

Maybe it's just me, but how Toy Story isn't in the top three of all these lists is astounding to me.  That movie is nonstop incredible, and easily the funniest other than maybe Incredibles.

Of the ones I have seen-

1. Monster's Inc
2. The Incredibles
3. Toy Story 2
4. Wall-E
5. Up
6. Toy Story
7. A Bug's Life
8. Finding Nemo
9. Cars

1. The Incredibles
2. Wall•e
3. Toy Story.  Funny and clever and a hell of an acomplishment CGI-wise. Remember the big deal made about Terminator 2's CGI only 4yrs earlier?
4. Finding Nemo
5. Toy Story 2.  Pretty much as good as TS1.
6. Ratatouille.  Looks beautiful and has some of the best animation of any Pixar movie but Linguini's too retarded.
7. Monsters, Inc
8. Up.
9. Cars.  When i saw the 1st teaser trailer i thought 'uh oh this is gonna be awful'. Then when Steve Jobs sold the damn company i thought 'he's selling before this flop comes out'. But i liked it ok.
10. Toy Story 3.  Just watched it. Meh. I didn't feel the fun and wonder from the 1st one. Nice ending.
11. A Bug's Life

TS3 just didn't hit me.  It didn't hit me NEARLY as hard as UP, where I was a grown man sitting in a theater wiping tears from behind his goddamn 3D glasses.

Nobody take this the wrong way, but what exactly was in TS3 that made it so emotionally powerful?  As Fig mentioned, I had some issues with the fact that it was essentially the same plot as the first two, but aside from plot beef I'm just not sure what was in that movie that people connected to so deeply.

- Branco

EDIT:  To answer the question, I'd go TS1, TS3, TS2.

1.) Monster's Inc.
2.) The Incredibles
3.) Toy Story
4.) WALL-E
5.) Toy Story 3
6.) Ratatouille
7.) Toy Story 2
8.) TIE: Finding Nemo/Up
10.) A Bug's Life
11.) Cars

This is a tough one. I legitimately love all of these films, excluding Cars, which I don't have any emotional attachment to. I really did grow up with these. Even though Up is fantastic, I'm not as attached to Carl and Russel as I am to, say, Woody and Buzz, or Mike and Sully. Cars is the only Pixar movie that I really don't like, and even that one is okay without the bar set by the others.