I'm vacillating between John Lee Roche and Eddie Van Blundht, both extremely entertaining in their own way. I'm going to go with Roche for his intensity, psychopathy and believability. I find those kinds of villains all the more terrifying for their realism.
My personal number three for season 4 would have been The Peacock family. They are just so disturbing and memorable.
Ronnie Strickland is my favorite from season 5. My number two is the Mothman, though I find it more interesting in idea than in execution.