a thought came to mind: RPG(J-RPG's in particular.) and Fighting games are the only genres i could think that have women/girls as the final boss.
the Tales and Final Fantasy Series has two.
Spoiler
Shizel and Atamoni/Void of Darkness and Ultimacea
Spoiler
Beatrice.
Samurai Shodown has Mizuki.
are there any other games, from different genres, that has a female final boss?