Roy Batty (Blade Runner)- This guy was such a weird and uncharacteristic villain that i couldn't help but love him. Also, he's probably one of the most unique looking ones i've ever seen, not because of an over the top costume or monstrous demeanor, but because the silver hair and blue eyes made him so realistic and close to his back story.
Christophe (The Truman Show)- The idea of this movie was one of the most original i've ever seen (for it's time), and while Christophe isn't your typical evil cruel bad guy, he's still an antagonist and a great one at that. I thought that the movie makers did a great job of painting an interesting and vivid character who didn't even need to be that important
Magneto (X men)-I remember that when i saw the first X men i was unimpressed by Magneto, thinking he was just some standard bad guy with a cool power. But when i saw X2 and witnessed his history then i thought he was a deep and original villain. He had motive and ideals that didn't even make him seem like the bad guy.