Angelus
When David Boreanaz first showed up in the first episode of
Buffy, it was pretty clear the guy had little to no acting exerpience or talent. Over the first season and a half he improved immensely, but it was when his character, Angel, turned evil midway through the second season of the series that he really began to shine. Angelus is sadistically evil, bringing torture and torment to an art form. He'll kill everyone around you, drive you insane in doing so, and rather than end your torment by killing you he'd make you into a creature like him, forced to suffer enternal torment. Lots of demons in the Buffyverse have made me shudder, Angelus is the only one I ever felt a feeling of dread when I knew he was coming up in the show.
The Operative
The nameless villian of the film
Serenity, he and his kind are dangerous not just because of their incredible physical abilities, but because they persue their missions with the single-mindedness and tirelessness of someone who truly believes what they are doing is right. Unshaken in that faith, The Operative does unspeakable evils to retrieve his quarry that is living amongst the crew of the ship
Serenity, killing any that he feels is necessary to get him closer to capturing his target.
Nina Meyers
Upon finishing the first season of
24 I had only one thought. I wanted to kill Nina Meyers. With my bare hands, preferrably.
Captain Hector Barbossa
I loved Barbossa because at the end of the day he was a sympathetic villian, which all the best ones are. While he was in opposition to the protagonists, his motivations were completely understandable. Reverse the curse, be able to live again; be able to taste and feel and simply enjoy an apple. His last line in
Curse of the Black Pearl is perfect in explaining his desire. "I feel...cold." He could feel again, even if it was death he was feeling. Basically, there's a reason why he came back and was so easily accepted as one of the heroes.
There's a couple more I can think of, but I'll leave them for later.
Also, this is what your posts in this thread should look like. Explain why they are good villians, please.