My top 3:
3. Emma Frost: The White Queen from X-Men fame. A very cold and beautiful woman, she had strong telepathic powers. (She later became one of the good guys, but I always liked her more as baddie). She was scheming (a necessary ingredient for my favorite villains), and her powers relied on her mind. I am a fan of smart villains. Plus, her coldness was a great counter to the emotional heroes (Wolverine, anyone?). I always like the detached villain, as well.
2. Magneto: Scheming (see above), efficient, ruthless - and he thinks he's the good guy! Well, perhaps not "good", per se, but history is written by the victors, right? Control over metal is a powerful ability, but also one that requires imagination if used for anything other than destruction. And more, he's got a personal tie to his greatest opponent - and that makes for great reading.
1. Doctor Doom: Yes, he's even better than Magneto. First off, he's wearing archaic-yet-ultramodern armor over his charred and scarred skin. Next, he's the ruler of a small kingdom, with his own army, teams of scientists, and killer robots. But even better, he's a mastermind in the truest sense. Smart, intelligent and a certified genius, he also has a classic archetypal weakness: his hubris. And more, this weakness is intimately tied with his greatest opponent, for if he had listened to Reed Richards, Doom would not have been deformed as he was. Other than Magneto and Charles Xavier, who respect each other, Doom hates Mr. Fantastic with a passion. Did I mention he's a megalomaniac, as well? Doom just has all the right contents to make into a raving, scheming, threatening, force of evil. He can be ruthless and cold, or turn passionate within moments. You want a villain who is larger than life? Here he is.