Bowser's definitely the best. Everything he does in any of the Paper Mario games is laugh-out-loud funny (except for Sticker Star, where he pretty much does nothing).
My least favorite is probably Daisy. She's the only character I can think of that's literally worthless. She has zero personality or reason for existing. Just another princess.
Honorable mention to Jr. Troopa. I was really bummed when he didn't show up in Thousand Year Door.
Currently playing:
Bloodbath Paddy Wagon Ultra 9