In the Mario games, I really like many of the Super Mario Bros. 2 enemies, like Mouser, Triclyde, Cobra, and Fryguy. I wish they would return for more games (though I think a green version of Cobra appears in Mario Pinball Land). I also like Chainchop and Firechop. Both characters don't seem to appear in very many levels of any game, but Chainchop at least does seem to be a bit popular with fans.
On Taz-Mania I like The Kiwi (such a cool design) and Wendell T. Wolf. Both characters weren't in many episodes, and Wendell is really funny.
And I enjoy Fowlmouth on Tiny Toons, especially his shouting. Shame he wasn't in more episodes.
On Darkwing Duck I like Tuskernini, though I am surprised they made an action figure of him but not Quackerjack or Negaduck. Then again, the Tuskernini figure was the first Darkwing Duck figure I owned (at a time when I didn't even know who the character was... Though I would have much rather had the Megavolt or Honker figures first).
By now I wonder if Lenny, Carl, or Comic Book Guy from The Simpsons still count as minor. They seem to have been used a lot more in the last several years. Otherwise, I like the look and voice of Professor Frink, and I also like Dr. Nick Riviera's voice. Troy McClue and Lionel Hutz are also on my list of favorite Simpsons characters... Phil Hartman did a great job with these characters, and the writers did a great job writing for them. And I also like Larry and Sam, the two barflies at Moe's who rarely get any of their own dialogue. Oh, and also Gil... Don't know why, but Gil's a great, funny character.
I assume this is limited to animated characters, right?