This is a LOT better than my list which I gave up making not even halfway through. Thank you, for making this!
You mentioned in the description that you are open to suggestions so here's my minor input.
- Cyberpunk 2077's description says that you can create a custom trans character, however, there's also a fully voice acted trans character called Claire, who gives you the racing side-quests that might be notable.
- Hogwarts Legacy also has a trans side character, the bartender called Sirona Ryan in Hogsmeade. It also lets you create your custom character as trans.
- It's not out yet but I've been paying attention to Goodbye Volcano High, which according to their FAQ has a non-binary main character called Fang. Source: https://goodbyevolcanohigh.com/faq/
- The Sims 4 and Baldur's Gate 3 both let you create trans custom characters.
I'm setting my list to private so as not to divert any attention from this definitive masterpiece.

@mesterjani Thank you very much for these!! I appreciate them a ton ♡
I actually was aware of the character in Hogwarts Legacy, but given JKR's history of transphobia and the fact that she considers monetary support of the HP series to be support of her bigoted views, I actually decided against including the game at all. I know she wasnt directly involved with the creation of the game, but I still felt giving the game any attention would still benefit her. Hope this makes sense, thank you again for your suggestions!

Hi, again! Thank you for including my previous suggestions, I hope you don't mind some more.
- The Comic Wheel Sisterhood has a character who is struggling with dysphoria and the main character helps her out. You help her choose her name from a set of choices, so I don't know what to call her canonically, but I'm pretty sure she's referred to as The Peppermancer.
- Starfield lets you choose any Body Type, Walk Animation, and even pronouns including they/them.
Spoiler?: There's also a female character called Hadrian who is originally a "clone" of a man. I'm not sure if she classifies, but I did see a bald white dude having an embarrassing meltdown over it on Twitter, so I figured it might be notable.

I promise I won't spam you with these. It's your list after all. I also understand and respect your reasoning about excluding Hogwarts Legacy. I hope I didn't come off as one of those people by suggesting it.

@mesterjani Hey there, no worries! I appreciate these a lot, so by all means feel free to spam me lol. And don't worry, I didn't think badly of you for suggesting Hogwarts Legacy, so you're perfectly fine :)
Thank you again, I'm sorry it took me so long to get back to you!!

Adding to Mama from Somnium Files, an exchange in the second game suggests she has had bottom surgery. In Exocolonist, some dialogue if you pursue the medical career implies Utopia is a trans woman, something the devs confirmed directly to me when I asked -> https://twitter.com/AKANEOWARII/status/1647246843699515392

7th Dragon 2020, at least in the English fan translation, features a sidequest from a "transfixing woman" to retreive her "blue pill bottle", which she says contains hormones that are very important to her. Additionally, an NPC in the sequel, 7th Dragon 2020-II, will greet the party with "Mr, Ms, Mx Murakumo!", implying that at least one member of the player-created party could be non-binary.

@lesbiankakyoin @LunaFlare thank you both! ♡♡

I have a couple of suggestions if that's okay, sorry if they're already present and I didn't see them. In Stray Gods: The Roleplaying Musical, the latest incarnation of Hermes is nonbinary. In Harmony: The Fall of Reverie, Nora is a trans woman and Yana, Chaos, and Truth are nonbinary.

@TabletopRPGFan It's always okay! Thank you so much ^__^ ♡!!

For a suggestion I didn't see on here, The Arcana allows you to be nonbinary, one of the romance options (Asra) is nonbinary and uses he/him pronouns, and several major side characters (Valdemar, Nazali, and Vulgora) are nonbinary with they/them pronouns. There is also a minor character, Scout, who mirrors whatever pronouns your character uses, which can include they/them.

I see you already have Heart of The House by them on here, and I have no idea how you'd feasibly list them because there are so many games, but if you're not aware having nonbinary/trans options and diverse characters aside from yours are the norm for any interactive fiction game published by Choice of Games or Hosted Games! Off the top of my head a few notable ones are:

- Creme de la Creme (protagonist can be nonbinary, all romance options can have their genders selectable or randomised which both include nonbinary)
- Fallen Hero: Rebirth, Fallen Hero: Retribution (protagonist can be nonbinary; one of the romance options (Dr. Mortum) is trans, whether a trans man or a trans woman or intersex will depend on what gender you selected them to be; a major side character, Hollow Ground, also does the same as Scout from The Arcana in that they mirror whatever pronouns your character uses)
- Keeper of the Sun and Moon, Keeper of the Day and Night (protagonist can be nonbinary)
- The Wayhaven Chronicles (protagonist can be nonbinary)
- Heroes of Myth (protagonist can be nonbinary; Min, one of the romance options and a major character, is nonbinary and uses they/them)
- Versus (protagonist can be nonbinary; Prince Everly, a romance option, is nonbinary with they/them pronouns; Breeze, another romance option, is either a trans man, trans woman, or intersex depending on the gender you select for them; Oli, another romance option, at first appears to be whatever gender you selected but turns out to be the false identity for a character named Dhanthik, who is nonbinary and uses zie/zir pronouns).

@HaloBlues thank you so much!!

hi, i made an account here just so i could comment two suggestions
- Limbus Company - The main character, Dante, uses they/them pronouns (and is not a player insert, despite what some people try to claim). IOS, Android, and Steam.
- Witch's Heart - This is a little bit complicated because the developer has confirmed that they did not intend for the character in question, Noel, to be trans and therefore it's not technically canon; however, they also said that people are free to interpret him as transmasculine and both a cis and trans interpretation of Noel is valid as long as people aren't nasty to each other about it. In the game, it's revealed that he was friends with the protagonist, Claire, when they were kids but as a child Noel was raised as a girl named Patricia. I get if you don't add this to this list because it's technically not canon as per Word of God, but a trans interpretation of him is very common. PC (available on vgperson's site)

For Va-11 Hall-A, you missed Alma's brother, Bernardo who is refrenced a few times in Alma's dialogue, including having to correct herself when almost saying all her siblings are girls, and mentioning him when talking about how almost everyone in her family got large breast genes, saying he got them when he was 8. It is believed he was only recently out hence why Alma had to correct herself. This was the first trans character I noticed after accepting myself hence why I remember him.

For Brawlhalla, the character Magyar also uses they/them pronouns although this is because they are literally 100 soldiers cursed to be reborn into whichever of their comrades are still standing at the end of battle, so I'm not sure if you wish to include that.

An addition (at least, I don't think it's there) I'd like to see is Runes of Pandemonium, a free erotic JRPG with anthological chapters. The protagonist of chapter 5 is a transwoman, named Christine, but starts the chapter closeted till they are reborn into a feminine-shaped cyborg. Spoilers from here: All protaganists in this game have shapeshifting abilities, and Christine was scared to use them in fear that they turn her into a man. There is a segment where she is captured and brainwashing is attempted. During this segment, you may visit Christine's memories from when she was in the closet, and she fights off the deletion program that is trying to erase them. Trigger warnings for this game: Chapter 1 has many depictions of sexual assault as that is how you access new forms in that chapter, Chapter 5 is tamer and more consensual in how new forms are gained, but there are still sus things in this chapter which are necessary to progress the story at times. The game also has cosmic/eldritch horror themes which might scare you. You may also skip to chapter 5.

Not a suggestion, I just want to thank you for making this list and adding the notes, it makes me very happy and feel less alone. :) <3

Even if I disagree with a few inclusions here, this is a massive list. Thank you for including examples of "bad rep." I was recently listening to a podcast discussing it and how transphobic inclusions of trans characters suck, but when they're modded out or localized away, the 'solution' to the problem has become erasure. Some of the most wince-worthy entries here reminded me of that.

I think you should add a warning to Yakuza 3's note informing that the original PS3 release contained a transphobic side quest that was removed in the remastered version (it involves a trans woman chasing kiryu down). It's probably important for those looking for a trans friendly game and accidentally play the PS3 version.

also I wanted to say thank you for this list, it's an amazing resource to help people find trans friendly games :)))))

this is a great list!! i've got a recommendation, too! fallout 76 features an explicitly nonbinary character named burke. they're the first nonbinary character to be featured in the fallout series, and according to the fallout wiki they were written by someone who uses they/them pronouns as well :) https://fallout.wiki/wiki/Burke_(Fallout_76)

Adding a suggestion:

Princess Farmer: The character Rowan uses they/them pronouns and has a nonbinary flag in their shop, and the "Mysterious Bunny" (later named Emby) character uses fae/faer pronouns.

(And for the Yakuza 3 entry, along with the warning suggested for the other substory, you should probably note that the substory listed is only in the Japanese version of the original game, it was cut from the original PS3 localization (along with a bunch of content in general) but is kept in the remaster)

Surprised to see Rain World on here without any mention of Ultrakill lmao
The character you play as, V1, is canonically genderless :)
And the angels are all non-binary, except for those who rise to power and essentially transition to a preferred gender identity like Gabriel (before his power is taken away and he's referred to by it/its by the other angels once more)
Also for Splatoon 3, Acht/Dedf1sh uses they/them pronouns in Side Order!

@skibidibiden @QTpitarianne @GlitchPirate @callmearcturus @NatalieZaki @blurry @Zanreo @CeceliAnonymous THANK YOU ALL SO MUCH!!! i truly appreciate everyones kind words and support!! This suddenly blew up on my tumblr so I'm sorry for addressing everyone here so late, but all suggestions have been added and adjusted!!

QTpitarianne, I unfortunately couldn't find Runes of Pandemonium in the search, but I will certainly keep it in mind!!

nova hearts has a nonbinary character in it's CJ !

@morgiebunned Thank you, the game has been added!

All good, that game is still in early access anyway (after around a decade) and is almost a third complete so it probably won't pop up here for a while.

Anyway, I forgot one: In the mature/adult visual novel 'Hush Hush: Only Your Love Can Save Them' (and is also in Blush Blush, but is more characterised here), one of the dateable side characters, Eli Kawase, is (non-binary) genderfluid, and likely uses any pronouns (though the game/media/players usually use he/him, and she/her is implied to be a mistake when used, referring by name is a safe bet tho as even Eli does this).
Eli wears a dress for a majority of the time on dates. On the first date with Eli, the player gets to ask about Eli's pronouns. in response, Eli explains that Eli is a new Eli every day, going from wearing dresses, going to the gym, etc. and doesn't actually say what pronouns are prefered.

Hi, saw this linked on Tumblr and thought you might enjoy some more additions:
-Dark Souls 1: The series' deliberately cryptic storytelling makes it impossible to make any definitive statement, but taking into account lore and design there are fans who interpret Gwyndolin as a trans woman. Still, it's all interpretative so you might wanna mention that.
-Dark Souls 2: This one is a bit unique in that it doesn't have a proper trans character but it does feature a coffin you can get into that changes the gender of the playable character. Might be worth mentioning.
-Labyrinth of Galleria: The Moon Society: A secondary character (Hubert) is a trans man who is later given a potion by the protag team to give him the body he wanted.
-Persona 5: Lala Escargot is depicted as a rather stereotypical "okama". Strictly speaking the more direct English equivalent would be a drag queen, but writing-wise could also be interpreted as a trans woman. Still worth considering, imo.
-The Last of Us Part II: One of the main characters (Lev) is a trans boy and his identity plays a big part in his story.
-Chicory: A colorful tale: Protagonist character is never referred to using gendered pronouns, but perhaps more noteworthy is how the translations into gendered languages allow the player to choose either male, female, or neutral pronouns for the player character.

@SpookSpark thank you, I have added your suggestions!
The Last of Us Part II actually was originally included on this list, however I decided to no longer include the title due to Neil Druckmann's support of Israel's genocide against Palestinians and the fact that the game itself is entrenched in his zionist views, and because of this I do not believe he should be supported by giving his game any attention. The description of this list has also been updated to reflect this (which I'm not saying as a dig at you specifically, just so that anyone viewing these comments is aware of this change as well thumbs up).
Thank you very much again for the other titles though!