For reference, all the little flag designs in their speech hearts are variant trans pride flags made for specific facets of the community.
Characters and their identities are listed from left to right.
Freddy Lupin, 100% Wolf, Trans Male, Fanon — I've fallen in love with this new little franchise, specifically that school TV series they've got going, but the fanbase is very small. Makes sense; it's nothing special, it's just something that pushes all my buttons the right way. Another fan introduced me to this idea, and their explanation made nothing but sense to me: when Freddy hits puberty, instead of becoming hypermasc and powerful, he becomes small and traditionally feminine. He spends the movie and series' runtime trying to prove himself a "real werewolf" who is just as tough and just as capable as any other. It's not a subtle headcanon, I know lol.
Eggs Trubshaw, The Boxtrolls, Non-Binary, Semi-canon — Laika tripped over themselves with this movie's LGBT rep, and that's a bummer because ParaNorman did a fantastic job with it. Snatcher's as Ms. Froufrou can easily be interpreted as reflecting meanspirited ideologies regarding trans women and AMAB cross-dressers, so I get it if any trans folks pass on this film. That said, Eggs is shown inuniverse as not understanding the sociological differences between men and women. The "proper boy" thing sounds more like his way of describing his human vs. boxtroll identity, not him proclaiming himself A Man. The trolls themselves don't have reproductive organs, either, so why WOULD Eggs identify as male, female, or anything else like that?
Trixie Lulamoon, MLP: FIM, Trans Female, Fanon — Yeah, lotsa the ponies are gay. It's hard out here for a conservative brony, huh fellas? LMAO. This headcanon has been popular since people who don't frequent 4Chan started watching Friendship is Magic, and it's one of those that has a lot of "evidence" to back it up; Trixie was male in early show concepts, she has one eyeshine (a stallion trait) instead of two (a mare trait), some of her transfemme fans think her voice sounds like she's going through MtF voice training, and she only really loses her mind over Twilight's phony magical amulet when she thinks it allows you to change others' genders. The list goes on!