I don't have a top 5, but here are some notable ones I loved.

Sephiroth (Final Fantasy VII)
Naraku, Sessahomaru, the Shikon Jewel (Inuyasha)
Kishin Asura (Soul Eater)
Death (Castlevania)
Virgil (Devil May Cry (Old games))
Venom (Spiderman)
Pyramid Head, Butcher (Silent Hill series)
Albert Wesker (Resident Evil games)
Demise, Girahim, Ganondorf (Legend of Zelda)
Jetsream Sam (Metal Gear Rising)