I'm this close to saying Goldfinger, but then the obvious answer becomes apparent.
Ernst. Stavro. Blofeld.
He built the best supervillian lair, ever (hollowed-out volcano), he had not one, but THREE great schemes (cause WW III, brainwash beautiful women to release toxic death, and blackmail the world with a diamond-powered laser), and he lead SPECTRE, which was behind the plots of three additional Bond films. And worse of all, he killed Bond's wife, Tracy!
He's also Bond's Moriarty in the original novels (where he killed Tracy there, too!)
No contest, really.