Not gonna count Ducky from LBT here, since we all know and love her already.
Starlight Glimmer has to take top spot as my favorite character in MLP:FiM and probably my favorite animal character in any cartoon. I loved her stint as a villain and her struggles to overcome her sociopathic tendencies to become a better person, and her friendship with Trixie breathed new life into both characters and let them become one of the best duos on the show.
Second place has to go to Mrs. Brisby from The Secret of NIMH. She's thrust into such a violent world and a harrowing storyline despite being one of the most vulnerable characters in the movie, but she pushes ever-onward through her fears to help the people she loves. She's resourceful, caring, and selfless, and 100% earned that happy ending the hard way.
And finally, I know this one's weird, but I love how the "Inspector Javert" role in Tangled is played by Maxwell the horse. The fact that the human constables won't listen to him, so he decides to go off and catch Flynn Rider all on his own adds a great dynamic to his narrative role and the challenges he has to overcome in his investigation. I wish they'd given him more to do in the series, they did a great job finding ways to keep Pascal the Chameleon relevant (another animal character I really like), but Maxwell was often relegated to the background.
