I went for a tie-in between Ganon(dorf), Zant and Dark Link.
In the end, I went for Ganon, because he's the main villain in a way. His look in Twilight Princess is my favourite, followed by the one in Ocarina of Time. He has a lot of backstory and a fair motivation for his evil goal.
I dropped Zant because of the way they made him near the end of the game. I love him as a villain because of his cool and badass personality. When you confront him in the Palace of Twilight, however, he suddenly becomes crazy and turns out to be like a spoiled kid. Shame. He would have been awesome as a main villain.
And Dark Link? Well, he's great as a dark character and occasional boss, and I love doppelgangers. The problem? He has practically NO backstory. Where did he come from? Was he created as a test by the gods, or by Ganon as a minion? He features as a final boss in Adventure of Link, yet that's the only time he appears in the game. So yeah, if there were a Zelda game with him as a main villain, I would choose him as my favourite, like Venom in Spiderman, Ninetails in Okami, Dark Samus in Metroid Prime etc.