In comics, I always answer Doctor Octopus.
(NB : I use the moniker of Grey Gargoyle because he is one of the few French characters of the Marvel Universe and because I like the Gargoyles cartoon).
In all of fiction, there is no name that immediately comes to mind.
Among the ones that I like in movies : Nosferatu, Joker (Nicholson & Ledger), Dracula (Coppola), the Strangers of Dark City, the Cenobites of Hellraiser, the Xenomorph, ...
The Cenobites weren't really villains though, were they? They were explorers in the dimension of pain and desire. Kirsty was able to reason with them the 3 times they crossed paths (movie 1, 2 and 6). Everyone else got on their bad side by messing with the status quo.