Comics:
Loki, from the Thor comics. Inspired.
Sinestro, from the Green Lantern Comics.
The Joker, the greatest ever.
Lex Luthor, the archetype of the mad scientist.
The Mandarin, from the Iron Man comics. Truly awesome.
Mephisto, from the Thor and Silver Sufer Comics.
As an aside, I think it would be great if they did another crossover of DC and Marvel, only this time, the villians fight each other, instead of the heroes. Lex Luthor vs Dr Doom. Now there is a comic I would pay for.
Movies/Television:
Aku, from Samurai Jack. No others (in this medium) can compare to the Deliverer of Darkness, the Master of Masters, the Shogun Of Sorrow, AKU.
Books:
Rimmer Dall, from the Heritage Of Shannara.
Pe Ell, from the same series.
Draken Korin (really, the Valheru as a whole), from the Riftwar Saga.