In no particular order:

10. Millenia (Grandia II)
9. Colonel Yoshiko Kawashima (Shadow Hearts)
8. Elvis (Perfect Dark)
7. Ganon/Ganondorf (various Zelda games)
6. Ridley (Metroid Series)
5. Samus Aran (Metroid Series)
4. Kazooie (Banjo-Kazooie)
3. Magus (Chrono Trigger)
2. Duke Nukem
1. Cardinal Albert Simon (Shadow Hearts)

Final Fantasy, again no particular order:

10. Kuja
9. Auron
8. Balthier
7. Amarant
6. Kain
5. Tellah
4. Galuf
3. Cyan
2. Kefka
1. Cid Highwind