Well this is probably a famous list, so might as well stick with it.
Captain Linebeck-So you all thought that Wind Waker had some humor in it? This man, is the king of humor in the Zelda Universe. Without this guy, well, Phantom Hourglass might as well be worse than Adventure of Link (sorry to AoL lovers out there). This guy had so much character to him as well, almost similar to that of Midna, except in a more of a lighthearted way. I don't think his cameo in Spirit Tracks was very inadequate, despite the fact that he improves the gameplay, but I just wanted more out of him.
Midna- Well you either gotta love her or hate her. But I just think she is the BEST sidekick out there. Ok, fine maybe Zelda and the King of the Red Lions was better, but you cannot argue that Midna is very amazing. She was just so cool. She helped you turn into a wolf, guided you (but one might argue that you got a bit TOO much guidance), and was your friend. I really cannot wait to see her in a new Zelda game (chances are very slim, but one can just hope).
Happy Mask Salesman- This guy is very, very full of enigma. I think there's more to this man, than the freak that was in Majora's Mask. You could even read Ganondork's article on him. Anyways, this guy had too little screen time in a game that, subtly, was supposed to be about him. This guy still has a chapter in his story that has not been told.
Anyways, those are my top three characters who should return in another Zelda game.