Wow, so many to choose from; but if we're going with "super" villains, as opposed to villains in general... I have to go with my boy, Dr. Doom.
Ever since I was a kid, I dug the armor and the fact that his name was Dr. Doom lol. How more "super villain" can you get than that?
In my teens, I started getting into DC comics, so eventually I was introduced to Darkseid...
but Doom will always be the first villain that pops to mind with people ask the question.
I would have said Ledger's version of The Joker, but everyone says that now adays (and with good reason)... so here's to not conforming for the sake being different.