The Boss (Metal Gear Solid 3), one of the few (male or female) characters in video games with character depth.
She is everything, a soldier, a mother, a mentor, a lover, a traitor and a hero, and above everything else, A BADASS.

Bayonetta is one of my favorite female characters ever. I vote for her.

Samus Aran.

For me it would be Samus Aran and Alyx Vance from Half life 2. Alyx is badass through the game.

1 - Maya Fey (Ace Attorney)
2 - Sierra Mikain (Suikoden II / Suikogaiden Vol. 1)
3 - Garnet til Alexandros XVII (Final Fantasy IX)
4 - Nariko (Heavenly Sword)
5 - Virginia Maxwell (Wild Arms 3)

Samus. She has destroyed planets before.

Edit: Oh, I also forgot Chun-Li! are we counting fighting game characters? If so, she definitely deserves to mentioned.

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Oh, another one that I forgot. Mai Shiranui! The hot-headed, ass-kicking Kunoichi!

Did anyone say Aya yet? Because Aya is the best. 

Curly Brace is the greatest