okay, many of u (who dont know anime that well, even those that do, might not understand my picks... i can explain them if needed)
1) L (Death Note) (i choose L cuz the protagonist is, in my opinion, kira... but some might consider Kira the antagonist to society cuz hes murdering people, lol... but thats not how its represented in the show) -also, depending on your viewpoint, the main char (kira) with his killing angel can be one as well, he would be tied here if u consider him a 'villain'- Very very very very intelligent, plotter, evil, sadistic, mindful, mindgames-- list goes on... EXTREMELY manipulative
2) Kefka (Final Fantasy) IMO, The most badass villain. he goes out and is genuinely openly evil.. merciless, ruthless. ( i would put sephiroth here as well, but i think hes too much a pretty boy. But he is pretty bad *** as well.)
3) Captain Aizen (bleach). Very manipulative, working behind the scenes, as well as kicking the **** out of those who try to stop him. He even fakes his own death, and acts innocent.
4) Darth Vader/Anakin: Well, he is definately evil, for sure. What good has he done? lol..
5) Ganon. **** him. lol. My first real villain, ocarina of time, so he gets it. Whenever anyone challenges him, hes like.. k.
Honorable mentions: Kerrigan (starcraft), Sweet Tooth (Twisted metal) and The evil general (in gears of war) (he kills your partner, slowly with his sword, and stands there, watching everyone run away.. and remember.. your a bad *** criminal in the game)