I'm only going to list only my top three non-video-game villains, because I don't have much in that catagory, but too much from video-games; anyways, I would have to say Captain Long John Silver from Treasure Island, Scarecrow from the Batman universe, and Kabuto from Naruto.
1. Silver just had a personality I couldn't help but like, despite (or maybe because of) the fact that he is a pirate. He was by no means a saint, but he was also quite humble, honorable, chivalrous, and fun-loving for a "bad guy". The way I saw him, he didn't want to be tied down to the law, but primarily took to piracy as a way to be free and cure his itch for adventure.
2. Scarecrow is, in my opinion, incredibly badass. Using fear as a weapon and as a mean to an end has always been an effective strategy, but he takes it to a whole new level by literally using it as a weapon to break his opposition's will. The fact that he's smart and resourceful enough to use such tactics coupled with the fact that his suit is hauntingly awesome just causes me to admire such an unscrupulous fellow.
3. Kabuto is truly one magnificent bastard. From almost the moment he appeared in the story (posing as a weak ninja from the Hidden Leaf Village) I felt that there was something about him I couldn't quite place and that I should keep my eye on him. Lo and behold, not only did he did turn out to be a spy for one of the village's most powerful enemy, he was that person's right-hand-man for being unnaturally intelligent (especially when it comes to anatomy, using it to exploit the weaknesses of the body) and just about stronger than anyone else in the village by using abilities centered around necromancy. My instincts to keep my eye on him also paid off well, as he is currently the longest living villain in the series (including his old master) and has been building up his strength quite a bit, only to resurface recently in which he shows he's got the balls to blackmail the true villain of the series into helping him. Despite all this though, he still maintains his composure, basically never letting himself act pompously or gloat like other villains would do, which is a fair bit why I don't seem to hate him despite how truly evil he is.