If you're talking greatest, it's hard to go past Doom. He's the quinessential meglomaniacal villain. He's all about world domination, defeating Reed Richards, and proving his inherent supiority over others. Doom's origin was recently retold in The Book of Doom miniseries, so if you're interested, that might be a good place to start.

Magneto would definitely have to be up there. He's a bit more 3-dimensional than Doom, and believes that everything he does is for the betterment of mutants. This leaves him with a lot more grey area.

I've always loved Ultron. He's a murderous robot Avengers villain whose obsessed with killing Henry Pym (original Ant-Man), his creator ("father").