Without a moment's thought, I would say... the Master. He's funny, but in a way I feel that I shouldn't be laughing. He reminds me a lot of Moriarty from BBC's latest version of Sherlock, and he and the Master as played by John Simm are my two top villains of anything. (Another of my top villains would be Smaug the Terrible, the villain of The Hobbit.)
I especially love John Simm's portrayal of the Master in the Utopia/Sounds of Drums/The Last Timelord three-parter.