These questions are slightly tricky. Not best. Not scariest. Not most evil. But favorite villain. Which is quite different.
Before 1970: Messala, Ben-Hur, 1959. The character who introduced me to one of my favorite themes - betrayal. And boy howdy, he's really got the corner on the betrayal market, and all just to get ahead in the world. Doesn't realize success will only take you so far, and friendship is one of the precious fragile things in life you can't take for granted. He also assumes Judah will think as he does, big mistake, and when he discovers that Judah chooses to protect his people over siding with the Romans, Messala feels a bit betrayed himself. Of course, he set himself up for that fall. I always liked that he investigated the rooftop accident himself, found Judah was telling the truth -- and then did nothing about it. Still miffed and and finding another way to success through Judah's fall. He really is out to win, which is perfectly demonstrated by the ruthless way he drives his chariot in the famous race. And then, he gets the best death scene ever. Judah Ben-Hur's journey through hatred and back would be nothing without a worthy antagonist, and Messala is that and then some. I've loved him since the first time I saw the movie.
Post 1970: Rene Belloq, Raiders of the Lost Ark, 1981. Ahhh, how I love Belloq. I'm particularly fond of bad guys who are one step ahead of the good guy, and Belloq was always a smart one. Well, until that minor misconception over what the ark would allow him to do. But the rest of the time, he's often ahead of Indy, and when Indy does slip ahead, Belloq figures things out and gains the upper hand again. I love that. He doesn't like the Nazis he works for, but they're useful, bringing him funding and manpower he wouldn't have otherwise, and so he tolerates them. He's also handsome and charming, something my favorite villains have in common.