Perhaps the Comedian from The Watchmen, because he was burly, incredibly cynical, raw evil, and worked for the government!
Soundwave is up there, because his voice was pure awesomeness.
Destro is on the shortlist too, shiny headedness is nothing to scoff at. He also had a snazzy uniform.
Ah, same with Zartan, as he does the same thing I do when I come in contact with the outside "AARRGHHH! SUNLIGHT!!"
Skeletor for his utter cravenness. You need a good whopping of cravenness for a supervillain.
And, btw, most of y'all LOSE for not stating WHY you chose who you chose, sheesh!