I would go with Darth Vader. I think the new trilogy kind've tore into the mystique he had. Seeing how he came to be the figure in the old trilogy made him more of sympathetic figure than a purely evil villain. Of course the old trilogy revealed him to be inherently good by the end of it, but the intimidation he posses in movies 4 & 5 is amazing. Heath Ledger's Joker is also a good contender, and it sticks out in my mind because the first time I saw The Dark Knight it blew me away, especially Ledger's performance.
Vader is a great choice and may have been my #1 choice if that ass-clown Lucas hadn't relegated him to the cheesiest movie cliche of all time! "Nooooooooooo!"
If only they had the guys who worked on The Force Unleashed game write the prequels. I loved the small details they included in his character, like how they didn't even give him a run animation.
How about Grand Moff Tarkin? In A New Hope, Vader is just following orders, and it seems (to everyone, the movie goers and the characters) that Tarkin is the real ring-leader here. Hell, he's the one who makes the call to blow up Alderaan after getting the (supposed) location of the rebel base, just for the hell of it. The man single-handedly wipes a planet from existence for shits and giggles (and to torture Leia more). Honestly, if that doesn't put him in the running, I don't know what does. Also dem cheekbones.
Good point. I feel Tarkin does have the real power but he just doesn't have that X factor, the intimidation that Vader has. Of course going along your lines of argument the Emperor could also be considered the best villain, since he also was directing Vader. I don't have a problem with that actually, he's one sinister, creepy looking mofo.