1. Sephiroth
2. Darth Malak

3. Albert Wesker

4. Ganondorf

5. Liquid/Revolver Ocelot

6. Death Adder

7. Reapers (Mass Effect)

8. Walter Simons

9. Kain

10. The Origami Killer

I left out Darth Vader & The Joker, as I believe they are better known as movie & comic-book villains than game villains, otherwise they'd have been in there somewhere.
Haven't played Starcraft, so I can't comment on Kerrigan. Although I have watched the cut scenes from Starcraft 2 & she's a great character. Wouldn't say she was an out & out villain though.