I suppose my picks would have to be:
Scar - cunning and power hungry to the end, full of ambition, envy and charm
Davros - creator of the daleks, interesting design, good take on mad scientist
Discord - capable of manipulating and discouraging the heroes in a matter of minutes, like his design
The Martians from the War of The Worlds - cold beasts that do nothing but wipe out the opposing military forces, but admit defeat when caught unprepared. Iconic machinery and weaponry