1. Kuroro Lucifer (HxH)
2. Hisoka (HxH)
3. AiZen (Bleach)
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The Millenium Earl (D. Gray-man) is definitely one of the best, he's a great villian yet he's so different, he has a villianous charm if you know what I mean.
Medusa (Soul Eater) trumps all the other villians in Soul Eater, she always manages to escape death and have the last laugh, its impossible for that snake to die. (in the manga atleast)
Eneru (One Piece) was the worst, he considered human lives to only be pieces in his contest and killed them like they were nothing, worst god ever. Simply because of the fact that he thinks and acts like he's a god makes him much worse than most of the Shichibukai and other villians in One Piece. (though Black Beard is simply awesome)
And an honorable mention would be Lelouch V Britania, though not considered a villian he's done enough villianous acts to be considered one.