These are my favorite anime villains of all time, these are my opinion. There are only one villain from each series and those I picked are the villains who I thought are the best in their series.
http://www.ranker.com/list/favorite-anime-villains/christiand-mulkey, other,
Shinobu Sensui
Yu Yu Hakusho
Shishio Makoto
Rurouni Kenshin
Light Yagami
Death Note
Homunculus (The Dwarf in the Flask)
Fullmetal Alchemist: Brotherhood
Gankutsuou
Gankutsuou: Count of Monte Cristo
Johan Liebert
Monster
Admiral Akainu/ Fleet Admiral Sakazuki
One Piece
Asura
Soul Eater
Vicious
Cowboy Bebop
Legato Bluesummers
Trigun