WESTERN ANIMATION
David Xanatos-What hasn't been said about this guy?
The Joker-Mark Hamil's performance, Nuff Said.
Mr. Freeze-Most tragic villain ever.
Darkseid-Most menacing villain in all the DC universe.
Maleficent-the definitive Disney villain.
ANIME
Frieza, Cell and Majin Buu-all three had a wonderful sense of menace and overwhelming power and each were unique. Frieza, haughty sadistic, power-mad and paranoid yet at the same time, extremely polite and courteous. Cell, calm, calculating, confident and creepy. And Buu was the perfect mixture between the absurd and the terrifying.
Vicious-Rarely has there been villain who appeared so little and speaks even less who leave such an unforgettable impression.
Light Yagami- the ultimate manipulative slimebag and hate his guts villian.
The Principality of Zeon- the quintessential totalitarian regime.
Sir Crocodile-the definitive One Piece villain.
Shinobu Sensui-Perhaps the most psychological villain in all anime.
The Sailor Moon villains- From the classic old-school villainy of the Dark Kingdom to the stylish grand operatic villainy of the Black Moon Clan to the otherworldly sci-fi villainy of the Death Busters to the bizarre and garnish yet psychological villainy of the Dead Moon Circus. Each were unique and fascinating.