i would say that being able to empathize with a villain makes them a bit more real and enjoyable to me. Bond villains would be an obvious example of this, as they are often men that just want to improve the world, albeit in a twisted way. So, for me, a villain with believable and, in a way, reasonable motives are the best kind. That being said:
Literature: Tie between randall flagg from the stand and napoleon from animal farm
film: Vader is an obvious choice, though i also liked old-school general zod or ciguhr from no country for old men
Kneel! Kneel before Zod!
Edit: Site, y u no let me caps lock?