Patient Gamers

If you accept games where you fully create the character, you've got a ton of RPGs. Baldur's gate, elder scrolls, arcanum, fallout.

I'll recommend a few from different genres:

• Fire Emblem: The Blazing Blade (later FE games also allowed the player to choose between male and female)
• Castlevania: Order of Ecclesia (or Bloodstained: RotN for a newer, but aging, game)
• A Hat In Time (not sure if this is really that old but it's an amazing platformed)
• any Touhou game
• Life Is Strange (again, not sure if you'd consider this old)

No One Lives Forever (and 2)

It's also rare to have a female protagonist in an FPS.

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.

Ms. Pacman :)

Wet is a fun game if you can handle the loading screens.

The Guardian Legend on NES.

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.

Saboteur 2 https://en.wikipedia.org/wiki/Saboteur_II:_Avenging_Angel

Metroid!

Venetica

A roleplaying game with a female hero and an interesting story:

https://store.steampowered.com/app/338140/Venetica__Gold_Edition/

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.

• Broken Age - point & click
• Little Dew - ARPG/Zelda-like
• most RPGs with character selection (Elder Scrolls, Mount & Blade)
• Raven's Hike - puzzle/platforming
• Shantae - platformer

I don't think anyone has mentioned this yet.

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.

One of my top 3 JRPGs, Star Ocean: The Second Story, has a remake coming out early November. In the beginning of the game, you get the choice to play as one of the main characters, a male or a female, each of whom has their own story arc and exclusive party members that can be found during the playthrough.

A bit late to the thread, but I just wanted to say Beyond Two Souls recently had its 10 year anniversary, if that counts as old.