Killian, by a long shot.
Killian is the only decent villain to go toe to toe with Iron Man, to be an actual supervillain instead of a Guy In A Suit, to actually insinuate himself into Tony's life over a long period of time, to conceive a brilliant subterfuge that deceived not only Tony but the world, and to have aspirations toward supervillainy that all the others severely lacked.
Killian - For being almost identical to Hector Hammond in the GL film. Slimy ugly weasel nerdy nobody, turned into superpowerful fearmonger.
I'm not sure you and I watched the same IM3 and GL. The only accurate descriptor you have of Killian is "nerdy nobody." Killian was neither slimy, ugly, nor weasely. He was nerdy in 1999, and crippled, but there was nothing there to insinuate that he was slimy or ugly, or even a bad guy. In fact, you can't help but feel sorry for that guy. And then what he turned into was a suave, sophisticated, brilliant and thoroughly vicious supervillain; not a psionic monster with a giant head.