1) Miranda Lawson: Mass Effect 2 - Perhaps the closest thing to a classic bond femme fatale on the list. She's got plenty of assets at her disposal and just for good measure can move things with her mind.
2) Morrigan: Dragon Age Origins: - She's dark, mysterious and can shapeshift into monsters. She also might be the single most important character in Dragon Age.
3) Bayonetta: Bayonetta - Perhaps the only 360 character capable of wrecking Kratos (Of God of War). She would probably do it to a dope soundtrack and a sucker in her mouth too.
4) Ada Wong: Resident Evil 6 - If you don't think Ada deserves a spot on the list just ask Leon. While her movie counterpart didn't quite do her justice, she never fails to disappoint in any of her game appearances.
5) Lilith: Borderlands - Pandora might have it's fair share of intimidating bad-asses but none of them can touch Lilith...and trust me they have died trying.