[Crazy Jetty]

To me, the best villains are the ones that are complex. And the ones that you can genuinely find yourself sympathizing with.
Which disqualifies most of the godlike villains, in my book. Apocalypse, Galactus, Dark Phoenix, while neat are pretty much maguffin characters. They're the big bads, the ultimate power, and the ultimate challenge for our heroes to overcome. And honestly, they don't really need to be anything more than that in order to be fun, and to work.

Magneto, Sandman, Doctor Octopus, Dr. Doom, the original Thunderbolts, to me are great villains. They're all very deep and complex characters.
But I'd choose Doom as top favorite.