A first attempt toward a feminist video game compilation. Comments are very much welcome. I'm not sure how to classify the games, really, but I'll give it a try, for clarity.
Games by trans people with trans themes:
Kims Story: http://www.freeindiegam.es/2012/11/kims-story-kim-moss/
Intake/Ten/Fall/Closet (Maddox Pratt)
Lim/Brace/A Synchronous Ritual/Terf War (Meritt Kopas)
Encyclopedia Fuckme and the Case of the Vanishing Entree (Anna Anthopy)
Reset (Autumn Nicole Bradley)
Galatea/The First Draft of the Revolution/Alabaster (Emily Short) Gender inversions, women in an oppressive world of men trying to find agency, and discussions of subject/object positions.
* Porpentine is a transgendered feminist video game artist with a lot to say about the state of games and gender issues, if not always very clearly, as is the case of Howling Dogs which has gotten quite a lot of attention and has inspired other feminist video game creators
* Experiment in queer fighting game mechanics: Queer Power (Molleindustria)
* To My First Born Son (increpare), a tribute to feminism and the future sons of the world.
Critiques/subversions of stereotypical masculinity and some problems these pose
Silent Hill 2/Silent Hill: Shattered Memories
Metal Gear Solid 3: Snake Eater
Braid (Jonathan Blow)
Silent Hill 3/Silent Hill (not really sure there's anything remotely feminist going on there, but I did enjoy the games very much!)
The Path (Tale of Tales)
* Homosexual couple therapy anyone? Radiator 2: Handle With Care (Robert Yang) is your game!
* Gone Home, which amongst other things tells the story of homosexual, teenage, awakening and love.
Games with well-written and/or strong female characters:
Life Flashes By (Deirdra Kia)
The Longest Journey
Beyond Good And Evil
Cirque de Zale (Rebecca Clements)
Spooks (Lively Ivy/Erin Robinson)
Nelly Cootalot (Alasdair Beckett)
Blackwell (series) (Dave Gilbert)
System Shock 2
Star Wars: Knights of the Old Republic II - The Sith Lords, which has Kreia, who is a totally awesome mentor and one of the most interesting characters in all video games I've played.
Psychonauts, which if I remember correctly has well-written female characters in general.