In no particular order:
1) Gray Mann (Team Fortress 2). His genius is only rivaled by his stupidity, yet they blend together wonderfully.
2) General Grievous (Star Wars). Who doesn't like an acrobatic-four-armed-sword-wielding-strategist who kills telepathic space wizards for fun?
3) Wile E. Coyote (Looney Tunes). Gray Mann but far more comical, the voice seals the deal.
4) GLaDOS (Portal). Homicidal AI's are always great.
5) Morgoth (Lord of the Rings). For context, he was the first dark lord, and he pretty much annihilated an entire race of powerful elves. Not to mention he was served by the Balrogs and giant dragons (You thought Smaug was big? Search up Ancalagon the Black), AND he destroyed the main sources of light in the world. Need I say more?
5) Click (The Property of Hate). Mainly for the creepy design.
6) Envy (Full Metal Alchemist). I would've put down Lust, but Envy can be so deliciously evil and manipulating. still won't forgive him for killing Hughes tho
7) The Barraki (I wonder). One of the main reasons why I liked these guys is their backstory (and actually having a good reason for obtaining the Mask of Life). Not to mention their clashing personalities constantly trying to use or backstab each other yet maintaining a shaky alliance. Pulled it off better than the Piraka IMO.
8) Seath (Dark Souls). Although technically not a villain despite going crazy and doing incredibly immoral stuff later, when you think about it, just about everything happened just because Seath wasn't born with those precious immortality-granting scales.
9) Trusty Patches (Dark Souls). Trust is in his name, so you can trust him, right?
10) Aku (Samurai Jack). Probably the best way to write a comical villain: one minute ravaging a city and killing thousands for the sake of his own pleasure, the next breaking the fourth wall by talking about the general pattern of Saturday-morning cartoons.