Not any one character but the Goron are delightful. They are so happy when you free their city, they are one of the few areas that dramatically changes and shows their appreciation for what you did.
Ganondorf wasn't developed that much and was kinda just tyranny, death, and despair from what I remember, but I liked the idea of a villain that won and now it was the hero that had to destroy the current world and make something new.
Link because his storyline in oot and mm is insane.
Also, shout out to the music box guy related to the song of storms. Iconic.
Kotake and Koume are pretty cool. Ganon's weird moms who can fuse into a giant woman? Yeah, they're alright. I loved their appearance in Majora's Mask as completely innocuous business owners in the poison swamp.