My favorite was Zant. I just love his split personality. Throughout Twilight Princess, he's the sinister type of villain. He's very calm, but very aggressive and evil. It was cool to see him appear throughout the game. Unlike a lot of other games, it's not the kind of thing where you see him near the beginning of the game, and don't really see him any until the end of the game. Zant makes multiple reappearances, just making me anxious for the final battle with him. Once you final reach him, and are ready for the showdown, he goes ballistic. It really surprised me, how his personality completely flip flops in a matter of seconds and all the sudden he's this spastic madman. The fight was certainly enjoyable. I've heard it being criticized a lot, but I thought it was a ton of fun. It was a surprise to see all his variations of the previous bosses, but the one on one sword fight at the end was the best part. It was epic, to say the least, and I found it a bit challenging, at least compared to how easy the rest of the bosses in the game were. But of course, he wasn't the final boss, as most of us know. Ganondorf came in, and I'll say I liked the fights with him, but I would've prefered that Ganondorf had no appearance in this game, at least not as the final boss, because I think Zant would just be that much more awesome. The final battle would've been a lot better if it was him, because it would've been 5 times as amazing as the Zant battle that was the penultimate boss fight (or fourth to last, I guess). But the whole debate about Zant not being standalone would be in a different thread.
As we know, Ganondorf is the main villain in the Zelda series. And he is an awesome villain. Better than most villains in any Zelda game. The only reason people dislike him is because of the amount of games he appears in. And I'll admit that I like it when a different villain appears, because Ganondorf gets a bit old, as "classic" as he may be. He'd be my second favorite. I'm not sure as to whether I like Ganondorf better as Ganon or in his human form, but I'd never had a game where I fought one of them (except for maybe FSA) where I was disappointed in the fight. I guess that it's more fun to fight Ganondorf 1 on 1, like in TP and TWW, compared to a lot of the Ganon fights. But OoT Ganon has to be one of the most epic fights in Zelda history.
My third favorite is Majora, or rather Majora's Mask, or rather Skull Kid being taken over by Majora's Mask. MM is my favorite Zelda game, without a doubt. And Skull Kid being such a great villain under the evil of Majora's Mask attributes to the many reasons MM is my favorite Zelda game. It's really cool how he uses the moon to threaten the safety of Termina, rather than just being one of those villains that's like "I'm going to destroy the world! Haha! That's all there is to it! I'll just sit there and wait for you to fight me, and make it unclear why you need to kill me"! It's amazing how the Mask takes a curious creature and turns it into a monster. The fight(s) against the Mask were very fun, and where a really cool challenge without the Fierce Deity Mask.
Fourth would be Vaati. Vaati has appeared in a few Zelda games, being FS/A and TMC. And Vaati wasn't disappointing. In FS and FSA, we only saw Vaati as being this big, dark, heartless beast. He was pretty fun to fight, but was kind of dull at the same time. I liked TMC because it gave us a little background on who Vaati really is, and how he's got a similar physical buildup to Link. He seems like a weak character at first, but his greed turns him in to the monster that we see at the end of TMC and in FS/A. The fights with him were amazing in TMC, and the music made it pretty awesome too.
I haven't finished OoA or LA, so I don't really know much about Veran or Dethl (I think that's his name?). As for the other two, Onox and Bellum, I like them about the same. Onox was kind of dull, he only appeared right at the beginning, and then right at the end when you face him. Although I do think his appearance is pretty awesome, how he's this big general with golden armor. The fight was very fun and challenging, and it was cool to see him in his dragon form as well as his normal form. Though as a character, he's kind of dull, as we don't really know much about him throughout the game.
As for Bellum, he's (it's?) similar to Onox. We don't even know who he is until a few dungeons in to the game, and even then we don't know much about him other than him being evil. The final battle with him was kind of cool, I guess, in that we finally get to see him. The first phase of the battle was cool, in how it used the two screens to make the arena huge, to show how big Bellum was in proportion to Link. His little gooey minion things got annoying, especially later in the fight when they kept on falling and falling on you repeatedly. I liked the second phase better than the first phase, easily. I've stated before in multiple threads that I like one on one sword fights, and the one with Bellum was decent. There wasn't too much to it, but I'll say I enjoyed it, and didn't really find it too irritating.
Zant's an easy overall favorite for me though. It doesn't really seem that possible for him to make another appearance in any Zelda games, but anything could happen, really. I'd love to see him as another villain in a future title, especially if he appears as the final boss, rather than just an important villain working for the real final boss (in TP's case, Ganondorf).