Does it really count if he's playing a real life monster, and possibly the most depraved of all real life monsters? I mean, no one had to invent him. I think very few writers could. Idi Amin makes Hitler & Stalin look downright cuddly by comparison.
Hm. By that extension, does Idi Amin himself (in easily my favourite documentary, General Idi Amin Dada: A Self-Portrait) qualify?
Ben from LOST, Morden and the Shadows from Babylon 5, Brother Mouzone from The Wire, Antwon Mitchell from the Shield, Brother Cavil from BSG (something about Dean Stockwell in that role makes Cavil the perfect villain) and BOB from Twin Peaks. For movies it would have to be Palpatine in Star Wars. Come to think of it, though, there are a ton of other great villains.
What difference does it make. Did the original question ask original movie character or was it just most intimidating movie character. Forrest Whitiker portrayed a real character in a movie, and did it really really well. If it doesn't count than fine, but I don't see why not.
Bill "The Butcher" Cutting from Gangs of New York would probably get my vote. As for TV, The Carver from Nip/Tuck was pretty terrifying, that is until you found out who he was.
The girl from Takashi Miike's Audition...deeper, deeper... And the random freaks villains and main leads in Funny Games, I Stand Alone, and all those insane films.