Ever played against a boss who happens to have mannerisms that are very silly and comical, and their idiosyncrasies and eccentric behavior gives you a snicker, chuckle, giggle, laugh, or a snigger? Post your favorite villain who is the funniest in your eyes, and they can even have a dark sense of humor while being serious when they need be with their enemies.
Zinyak from Saints Row IV - (Honorable Mention: Great Mighty Poo from Conker's Bad Fur Day)
He is quite funny since he has a British accent and being a fan of literature, and at the near end of the second mission he has began beating the leader of the 3rd Streets Saints down while laughing and toying with him on how much fun he is going to enjoy breaking him. He is even quite a funny singer when he interrupted the duet between Boss and Pierce singing Biz Markie's "Just A Friend."
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Given that I have a darker sense of humor, I'm going to go with Dr Steinman from Bioshock.
EDIT: Forgot Glados from Portal who is easily the most amusing villain I've gone up against in a game.