Okami
Patient Gamers
A gaming community free from the hype and oversaturation of current releases, catering to gamers who wait at least 12 months after release to play a game. Whether it's price, waiting for bugs/issues to be patched, DLC to be released, don't meet the system requirements, or just haven't had the time to keep up with the latest releases.
^(placeholder)^
No One Lives Forever (and 2)
It's also rare to have a female protagonist in an FPS.
Ms. Pacman :)
Metroid!
Super Hang-On had a female protagonist but you only found out if you beat the hardest arcade mode
Cult: Heretic Kingdoms
Fantastic RPG game, with a badass female protagonist.
Wet is a fun game if you can handle the loading screens.
Eien no Filena on the SNES/SFC (it was Japan-only but it's been fan-translated).
Not only is the protagonist a woman - that fact is repeatedly plot-relevant.
Erica
The Syberia Series
The Longest Journey
Gone Home
Virginia
What remains of Edith Finch
Beyond Good and Evil
Gabriel Knight 3 has shared protagonists that you switch between; one is a woman.
Likewise some of the Broken Sword series
Talos Principle is either non-gendered or whatever you want the protagonist to be.
The first Blair Witch game from 2000
Everyone's gone to the Rapture
Also, holla at whoever said "No One Lives Forever"; that game rules.
I feel like no one has mentioned Urban Chaos till now. I friggin loved that game! The hacks too!
Final Fantasy 6. There are technically several protagonists, but the one with the better claim to "main protagonist" is a woman.
Also, Heaven's Vault isn't an old game, but it's not very well known or talked about, so I'll throw it in anyway.