Oh wow greatest villain, not necessarily the scariest. Hmmmmm.
I admit I thought Heath Ledger was a fantastic Joker. Far better than any ever portrayed on screen. People tend to forget how scary comic book villains were meant to be.
I also thought Alfred Molina made a very passable Doc Ock in Spiderman 2. Stephen Lang was a villain everyone could hate in Avatar. Most of the Disney villains were very good at what they were.
Hugo Weaving was a very good villain in The Matrix movies. I liked Samuel Jackson as the villain in Unbreakable. I know there are many more.
Gale