So many girls and women, from thousands of games, both famous both niche, I'll list some, otherwise I would never end, I like them more as full-fledged characters due to their background and attitudes.

Sengoku 3 (2001) - Okuni

Fallout - Tandi (Young), Cass (FNV),

FF8 - Edea Kramer\Ultimecia

FF7 - Scarlet

Silent Hill 2 OG - Angela

YuGiOh Card Games - Many female cards, Amazoness Archetype and Harpie Archetype especially

Breath of Fire Series: Deis

Ace Attorney Series: Kay Faraday, April May

Alpha Protocol: Sie

7th Dragon Series - Female Trickster

Wild Arms Series - Edna Warren

Dragon Quest Series - Maya and Menia

Guilty Gear - Dizzy, Jam,

FF9 - Lanì, Marilith

Megaman Battle Network - Lilly, Mrs. Mari,

Policenauts - Meryl (way better than her MGS incarnation)

Street Fighter Series - Mika, Elena, Ibuki

Fire Emblem Series - Echidna, Amalda, Titania, Lute, Nuibaba (Gaiden Remake), Ninian,

FF4 - Valvalis\Lamia\Arachne (introduction to Monster Girls)

FF10-2 - Berserker Yuna

Megaten Series - The female goddesses and daemons

Magical Drop Series - Empress, World

KOF Series - Shermie, Vice, Li Xiangfei,

Fighting Layer - Lan Yinghua

Fighter Destiny 2 - Adriana and Mei Ling

Shadow Hearts - Koudelka, Shania (especially her "Tatanka" spirit form)

Splinter Cell (OG Xbox) - Enrica Villablanca

Onimusha 2 - Takajo

Tenchu Shadow Assassin - Tagami

Metal Gear Series - Naomi Hunter, Venus, Teliko, The Boss

Chrono Trigger - Queen Zeal

Chrono Cross - Riddel, Steena, Leena, Janice,

SFEX - Sharon, Pullun,