I voted for Ganondorf, Vaati and Dark Link.
Ganondorf, is just THE classic villain. As games with repeat antagonists go I think he tops all. His Genius and Power make him an exceptional character to play against and to look into. His personality (or the little of it that we get to see) is unique. For example in WW, I never thought of him as smug unlike other villains, he never seemed entirely certain of his victory, it was as if he accepted he must battle Link and made no effort to thwart his plans to assemble the ToC, just waited for battle he knew must happen. Seemed to me like he almost had compassion.
Not that, but unlike other repeat villains, Ganondorf is very serious, and his plans always seem respectable which is completely contrary to say Bowser who is more of a comical presence and never really stands any chance of success. In fact, there are several occasions where it's possible Link would not succeed, but does through the help of others, I.E Zelda. This makes everything all the more interesting as it shows that the two are infact almost equal, and potentially if there were to be a twist in the series, Link could lose.
My second choice is Vaati who is not necessarily my second choice and it perhaps actually my first. This character seems very dark and impulsive. His plans are thrown together almost at random, for example, in MC when the chest doesn't contain what he is looking for after the sword competition, he appears to make his mind up on the spot and target the princess. Not only this, but we know a lot less about this character, and he seems to have great potential, for example, Ganondorf can only really change into Ganon, but Vaati seems to be able to take whatever form he wants, I find this interesting and it makes me long for a 3D battle against him as i'm sure he could take on some spectacular forms.
Finally, I have a lot less to say about Dark Link and just genuinely like him because it's an old idea, having to face the evil part of yourself, but I'd never seen it portrayed the way it is in Dark Link. Also, the fact that he is the evil from Link means that he is pure evil, and there is no chance of him having a good side. It's a character I and I'm sure tonnes of others, want to see a lot more of.
. I also voted for Zant, Vaati, Agahnim, and Majora. Even I forgot to voted for Agahnim he's a pretty cool villan. I never played MM, but Majora is an intense villan to defeat
