Thomas from Deadly Premonition
Hmm, I'd personally argue that Thomas isn't a tranny, at least not in the traditional sense that he personally identifies as the opposite gender. I think that Thomas is simply a gay man who has such a low sense of self-worth that he's willing to do things that he doesn't find any personal enjoyment or comfort in because it makes someone else happy. He doesn't dress as a woman because he wants to be one, he dresses as a woman because Sheriff Woodman is in the closet about being attracted to men, so Thomas is willing to "be a woman" when they fuck in order to make him happy, to his own detriment.
This is a surprisingly common character archetype in Japanese media, that westoid troons naturally always lump in as being """trans rep""" because they're clueless to the fact that having these characters who are clearly groomed into the role of pretending to be a woman makes them look worse.
Other examples are Chihiro from Danganronpa, a character who explicitly identifies as male but dresses as a girl because he thinks he's too weak and pathetic to be a guy, and so lives an explicitly unhappy life pretending to be a girl because of what he perceives as societal norms, and all his character development scenes before his death are him trying to become stronger and more masculine so he can shed this identity he's hiding himself in.
There's also Bridget from Guilty Gear, the archetypical example of this, a boy who's forced by his parents to pretend to be a girl because his village has a superstition about male twins being cursed, and should be put to death, his entire character arc is about how he can resist the shackles put upon him by society and the fact that even though he's so small and feminine, he is still a man and shouldn't be limited by how the world sees him, only for them to continue his story from the
BAD ENDING of the previous game, where he gives up and says "yeah I guess I'm a girl, sure", because trannies see a guy dressed as a girl and immediately claim them as troon wankbait, not realising the bad look this groomed child gives them.
The last example that comes immediately to mind is Luka from Steins;Gate, who once again, identifies fully as male, but has a crush on the protagonist Rintaro, who is straight and likewise struggles with his attraction to Luka despite being perturbed by the fact he's male. When Luka asks Rintaro to send a time travel email to his mother telling her to eat vegetables while pregnant with him so he'll be born as a girl (absolutely incomprehensible anime logic, but regardless), it's not because he WANTS to be a girl, it's because he wants Rintaro to be attracted to him and knows that the only way this will happen is if he's a girl, therefore his desire to be with and make Rintaro happy is more important to him than his own personal comfort in his own body. When the timeline gets reset, Luka isn't sad because "I won't be a girl anymore", it's because "Rintaro won't want to date me anymore", and the character growth he develops is meant to be that he has value whether or not the guy he likes likes him back, he should be happy regardless. But no actually he's a tranny because I think about him when I'm dilating and if you say otherwise that's trannyphobic.
The biggest irony about these sorts of characters is that they actually would work better as representing pooners, but naturally that never happens because troons run the place and is any little dood tries speaking up, "she'll" beat "him" down with that hulking shebeast tard strength
