Favorite Ganondorf: WW is actually my favorite. I disagree about saying he's the same as his OoT and TP incarnations, because while they are all the same character, they're also all different due to their experiences from the split timeline. OoT is young and cocky, TP is bitter about being sealed away but now has a bit more of a god-complex due to the Triforce of Power saving him, hile WW's Ganondorf is wiser and more reflective since he was defeated by Link, making him a bit more humble. WW for me is the first entry to actually try to make Ganondorf feel like something more than the token bad guy, so he wins out for me.
Favorite Zelda: Spirit Tracks, easily. I absolutely appreciate how she was made to be a subversion of previous Zelda's and how often she's used to poke fun at Zelda's bad reputation among fans of the series.
Favorite Link: Probably the toughest for me. I feel the manga adaption of Link fro LttP has really colored my perception of him in that game, so I've always had a soft spot for the Hero of Legend, especially when you see him again in Link's Awakening. Though I also really liked his incarnations from WW and TP. Both feel really put upon, but I love the fact that both are motivated by more than just saving Hyrule with TP Link slowly discovering his unknown destiny as the descendant of the Hero of Time, whereas WW Link spends most of his game trying to earn the blessing of the gods because no matter how much he accomplishes, they still don't think he has what it takes to fill the shoes of the Hero of Time, which is really fitting when you think about WW's reception and how much the fanbase loves OoT in comparison.
Favorite Side Character: I don't want to pick companions, because that's too easy, instead I'm thinking just a minor NPC or maybe someone plot important, but not a companion. So Marin from Link's Awakening is one of my favorites in the series.
Favorite Non-Ganon Villain: There are not many to choose from, but I may give this to either the Nightmares in LA, which really turn your head about your actions in the game. You have to kind of see them as a collective consciousness but they really added to the story. Majora is also a safe bet since their prescense is felt throughout the game and I love the mystery surrounding their origin and motive. Finally Hilda from ALBW, who is more of a anti-villain but something not seen very often in the fairly black and white world of Hyrule.
Favorite Soundtrack: Either Ocarina of Time for mostly solidifying the OST of the series or Twilight Princess which has some really groovy pieces like the Mian Theme and Midna's Lament. Though iconic themes like Zelda's Theme, Lost Woods Theme, and Ganon's Theme all debuted in A Link to the Past, OoT's versions are probably the most well known incarnations and they added a bunch of themes that have been remixed into future entries.