Patient Gamers

Super Hang-On had a female protagonist but you only found out if you beat the hardest arcade mode

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)

Ms. Pacman :)

Fatal Frame
Rule of Rose
Clocktower (the series, but I recommend 3)
Resident Evil
American McGee’s Alice
Fear Effect
Dino Crisis

Depending on your definition of “older” you also have:
Alien: Isolation
Fran Bow
What Remains of Edith Finch
Life is Strange

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.

Venetica

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

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

Metroid!

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.

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.

Most of my suggestions were already mentioned, but PN03 & darkened skye come to mind.

Pedantry aside, if you count the option of selecting a female character, trickstyle, borderlands, super mario bros 2, vigilante 8 second offense, tony hawk 3 (4, underground and probably any in this series but I haven't played them lol)

Trying to think of some obscure, unknown games: Eien no Filena, a JRPG on the Super Nintendo. The protagonist is a woman pretending to be a man as a lower class citizen forced to be a gladiator. Awkwardness ensues when she is "assigned" a wife and the men around her start being very confused about their sexuality.

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

I feel like no one has mentioned Urban Chaos till now. I friggin loved that game! The hacks too!