A good choice, but the greatest villain in Doctor Who history (and I've seen all of them) is unquestionably Tobias Vaughn from
The Invasion. It's technically a Cyberman story, but he absolutely steals the show.

"They can't harm us, Packer. We're in control...or at least I am."
There are a number of great villains I could go with for my #1, any number of which could conceivably be number one (including several from
Doctor Who). I'll go with Frank from
Once Upon a Time in the West, one of the best westerns ever made. Henry Fonda goes against type to play an utterly ruthless honoured user, and it may be the best performance of his career.