I think I'd have to give it Kai Winn. Her personal adgenda masked behind her faith. I think DS9, as a whole, had some top quality villains (Gul Dukat, Kai Winn, The Dominion, Sloan - and may minor ones besides) and these were able to be developed a little more due to the shows static nature. I'd also like to give an honourable mention to 'The Holodeck' - as the collective 'it' seems to cause no end of trouble for just about everyone who uses it. Also to the M-113 'Salt Vampire' - mostly as it's the first one a really remember atching the show as a kid.