This is a really hard choice... Ghirahim is cool for many obvious reasons.
However, I did love Ganondorf from TP, the way you have to beat him 4 times and every time he just changes the fight type and isn't even slightly, like, tired or wounded or something. Plus the way he dies is great.
Zant is such a powerful guy, and your main enemy throughout the game, and turns out to be an insane maniac.
Though I'm not really a fan of him, he is indeed a very unique character.
I think I'll go with Bellum... simply because he's cool. He's an evil monster. Being. Thing. He's described as an "evil phantom", and he is a gooey squid with an eye in the mouth, completely invincible except if you strike his eye with the Phantom Sword. (Which implies that he is invincible to the Master Sword!) He also never speaks, and he is powerful enough to defeat the Ocean King - maybe implying some kind of intelligent beast, with completely evil intentions. Plus he has the power to possess people and things - not just like a lot of other villains posessed Zelda in various games, but he can possess ships and have them grow eyes like his own, and he can transform people into phantom-like knights, and he can simply use life force sucked out of normal people to create invincible knights and terrifying monsters.
Plus, I know no-one else is gonna vote for the DS games, so I might as well do so.