In the Original series, my favorite villain was Ghostfreak. First, he was my favorite of the original 10 aliens, but I always felt that he was different from the others. I was surprised to see I was right.
I think Ghostfreak's a good villain in general and I enjoyed his arc where it revealed that all those monster-aliens were his underlings, but for the most part it's because he was my favorite alien.
Found Khyber's home world and species name- link text
I like this kind of backstory, mostly because it isn't something that's cliche to the type of character Khyber is(like say, he comes from a species/family of hunters). Instead, Khyber's people live on a basically all around crappy planet, with his species(Zaroffians) forced to make a living by mining. Those who escape live on to become some of the most feared individuals in the galaxy. Interestingly, most Zaroffians that get off-world become warlords and criminals, but Khyber decided to pursue hunting.