I have a lot more favorite characters in each film, but I’ll boil it down to the best ones.
Toy Story: Woody, Buzz and Jessie
A Bugs’ Life: Flik, Heimlich, and Francis
Monsters Inc: Mike and Sully
Finding Nemo: Marlin and Dory
The Incredibles: Helen, Violet and Edna
Cars: Lightning McQueen, Mater and Sally
Ratatouille: Remy, Linguini and Colette
Wall-E: Eve and Wall-e
Up: Dug and Russel
Choosing favorites is hard, but I’ll give it a try:
Toy Story: Rex, Buzz
A Bug’s Life: Dot, Heimlich
Toy Story 2: Rex, Bullseye
Monsters Inc.: Boo
Finding Nemo: Dory
The Incredibles: Edna, Violet
Cars: Mater
Ratatouille: Remy
Wall-E: Mo
Up: Dug, Russell
Ooh, I want in on this.
Toy Story: Ducky! 
(Don’t ask why - I guess I just find those quacking noises he makes whilst trying to reach the doorbell to be so endearing)
A Bug’s Life: Slim (he’s voiced by David Hyde Pierce, which is about as good as it can possibly get.)
Toy Story 2: Stinky Pete (check that - being voiced by Kelsey Grammer is as good as it can possibly get.)
Monsters, Inc: Sulley
Finding Nemo: Gill, Bubbles, the Angler Fish
The Incredibles: Bomb Voyage
Cars: Doc Hudson (R.I.P. the great Paul Newman)
Ratatouille: Remy, Anton Ego
WALL-E: Wall-E, Eve
Up: Alpha
Toy Story: Woody
A Bug’s Life: Francis
Toy Story 2: Rex
Monsters, Inc: Mike
Finding Nemo: Deb
The Incredibles: Edna
Cars: Luigi
Ratatouille: Ego
Wall-E: M-O
Up: Dug
Toy Story 3: Ken
This was so much fun to fill out! I never realized how much I liked certain characters, such as Deb.
I only picked one for each film, though Frozone, Eve, and almost every other character in Monsters were very close to making it on.
Toy Story: Hamm / Slinky
A Bug’s Life: Flik / Atta / Heimlich
Toy Story 2: Jessie
Monsters, Inc.: Mike / Sully
Finding Nemo: Dory
The Incredibles: Dash / Violet / Kari (how ever you spell it)
Cars: Mater
Ratatouille: Remy / Emile
WALL-E: WALL-E
Up: Dug
Toy Story: Woody
A Bug’s Life: I don’t remember well, but I guess Flik
Toy Story 2: Jessie
Monsters, Inc.: Sulley
Finding Nemo: Dory
The Incredibles:Bob and Helen
Cars: Lightening McQueen and Mater
Ratatouille: Colette
WallE: WallE and EVE
Up: Dug
Toy Story: Woody, Buzz Lighyear, Jessie, Bullseye.
A Bug’s Life: Flik
Monsters Inc.: Sulley, Mike, Boo
Finding Nemo: Nemo, Marlin, Dory and Crush
The Incredibles: Dash Parr Jack Parr, Bob Parr
Cars: Lightening McQueen, The King, Doc Hodson
Ratatouille: Remy
Wall-e Wall-e, Eve, M-O
Up: Carl Frederiksen
Toy Story: Woody, Buzz, Slinky, Rex, RC, the LGM
A Bug’s Life: Flik, Dot, Hopper, Heimlich, Rosie, Tuck and Roll, the two flies
Toy Story 2: Woody, Buzz, Jessie, Big Al, Bullseye
Monsters Inc: Roz, Sulley, Mike, Boo, Randall
Finding Nemo: Nemo, Marlin, Dory, Crush, Nigel, Gill
The Incredibles: Bob Parr, Helen Parr, Syndrome, Mirage
Cars: Sally, Mater, Doc Hudson, Flo, Ramone, FIlmore
Ratatouille: Remy, Emile, Linguini, Colette, Gusteau
Wall-E: Wall-E, Eve, M-O, AUTO, VN-GO, PR-T, VAQ-M
Up: Carl, Russell, Charles, Dug, Kevin, Alpha
Toy Story: Woody, Buzz, Rex, Hamm, Mr. P.H, Slinky
ABL: Flik, Dot, Atta, Heimlich, Dim, Queen
TS2: Jessie, Bullseye, Wheezy
Monsters, Inc: Sulley, Mike, Boo, Randall, Roz(lol)
Finding Nemo: Nemo, Tank Gang, Darla, Marlin, Dory, Seagulls(mine!)
Incredibles: Violet, Jack-Jack, Frozone, Helen, Bob, Dash, Tony, Kari
Cars: Mcqueen, Sally, Mater, Doc, Mack, Filmore, Lizzie
Ratatouille: Colette, Remy, Linguini, Emile, Gusteau
WALL.E: WALL.E, Eve, Captain, AUTO, Cockroach, MO
Up: Carl, Russell, Ellie, Dug, Kevin, Muntz
The cockroach’s name is Hal, for future reference. Heehee, you like all of them, don’t you? Mirage seems to be pretty popular, but she still gets under my skin. Nice list, Ami 
Thanks very much, IV! There’s many more characters I’d like to mention, including Mirage, but I’d be here a while! And thanks for telling me Hal’s name 
No prob, Ami
WALL-E: You guessed it, WALL-E
Toy Story: Jessie
The Incredibles: Helen
Up: Dug
Monsters Inc. Mike
Nemo: Dory
Bug’s Life: Francis
I haven’t seen Cars or Ratatouille yet.
TS/TS2: Buzz
ABL: Slim
MI/MI2: Mike
FN: Marlin
TI: E
Cars 1&2: McQueen
Ratatouille:Linguini
WALL-E: Captain McCrea
Up: Dug/Muntz
TS3: Ken
EDIT: after seeing TS3, Ken is my favorite character in the film by far.
Toy Story: Buzz and Woody
A Bug’s Life: Heimlich
Monsters INC: Mike
Finding Nemo: Crush
The Incredibles: Bob, Helen, and Jack-Jack
Cars: Lighting McQueen
Ratatouille: Haven’t seen enough of it.
WALL-E: WALL-E and EVE
UP: Carl and Ellie
Oooh, dude; you really should sit and watch Ratatouille one day. It’s really enriching, funny, and more than its 2 hours worth.
New List!!!
Toy Story: Woody
A Bug’s Life: (I bought and watched yesterday!!!) Flik, Rosie, Gypsy, and Manny)
Toy Story 2: Jessie
Monsters, Inc.: Sulley
Finding Nemo: Dory
The Incredibles:Bob and Helen
Cars: Lightening McQueen and Mater
Ratatouille: Colette
WallE: WallE and EVE
Up: Dug, Russell, Ellie, Kevin, CARL!!!
Toy Story: Ooo. Toughy, though, toughy. I guess Rex. I’d love it if he said “inconceivable!”
A Bug’s Life: Manny and Gypsy
Toy Story 2: Toughy again. Jessie, then. I got a Jessie costume from my grandma and wore it to Disneyworld X3. And I still have the autographed doll!
Monsters, Inc.: Randall. I kinda owe it to him for sparking my reptile love
Finding Nemo: Gill
The Incredibles: Toughy again. Kari (thanks for the reminder, Incrediblegirl) “THE BABY WAS EXPLODING!!!”
Cars: I really liked Ramone and Flo when I saw it, but I’m not sure anymore
Ratatouille: Alfredo Linguine. That name is just hilarious:lol:
Wall*E: Wall-E. This is the only time the hero of the story is my favorite character O_O
Up: Russel, Kevin, Kevin’s babies
Jack-Jack’s sitter is Kari. Welcome, Esmedes!! Konrad, you should update your list since you’ve seen Ratatouille now
Toy Story: Sid, Mrs. Nesbit
Bugs Life: Hopper
Toy Story 2: Stinky Pete
Monsters Inc.: Randall, Boo
Finding Nemo: Gill
The Incredibles: Syndrome
Cars: Doc Hudson
Ratatouille: Anton Ego
WALL-E: Auto
Up: Muntz, Kevin
Hmm, I’m noticing a pattern… 