Let's see... what if anything on my list actually made it?
1- Speak from The Tick. It was just so unexpected that they kept him. And then the capybera reveal. And just... looking like that.
2- The catterpuppy from House 2. This thing is just entirely too adorable.
3- Jones from Johnny Mneumonic. I know The Matrix is the only Kean Reeves cyberpunk movie from the '90s we're supposed to care about but HACKER DOLPHIN.
4- Blanka from Shadow Hearts Covenant. Just a random wolf, in your party, being Solid Snake and having epic showdowns with wackier wolves.
5- Mao from Shadow Hearts: From the New World. A very large house cat with a drinking problem who knows kung fu and works for Al Capone.
6- Brain from Inspector Gadget. The real hero of this story.
7- Swift Wind from She-Ra. Here's just this talking horse who's kind of a useless jerk, but we're still making him a senator, or something.
8- Mousely from A metric truckload of arbitrary Resident Evil 4 fan art. It's a cute gimmick. Someone mod this in already.
9- Link from Zelda: Twilight Princess. Or should I be listing Midna? One of the two is the brains and the other's a furry weirdo, you sort it out.
10- Sir Didymus and/or his noble steed Ambrosius from Labyrinth. Just... good times.
11- Ace from Batman Beyond. It's just nice that Old Batman has this cool dog around.
12- Slimer from The Real Ghostbusters. His status as an animal is questionable but he opens his mouth and Frank Welker noises happen so I count him.
13- Tracy from the not-real Ghostbusters.
14- Scooby Doo from the same.
15- Madcat from Inspector Gadget. Just, you know, here's a cat. Who's evil.
16- Jonesy from Alien.
17- The mice from Voltron. I don't think they really qualify as separate characters.
18- Jillas from Slayers Try.
19- Nibbler from Futurama.
20- Bronx from Gargoyles.
21- Jabberjaw from same.
22- Hanpan from Wild ARMs.
23- Nall from Lunar.
24- Felicia from Dark Stalkers. I guess the terrible cartoon specifically.
25- Comet from Supergirl.