First one that comes to mind is “The Outcast”. Not really gay, but for anyone who is triggered by anything different they would consider it “woke”.
There’s also:
-
The Host which has Crusher dealing with falling in love with a Trill who moves hosts. It can be seen in some very specific ways as a trans allegory and just challenging heteronormative assumptions about love and attraction.
-
The show really pushes a lot of ‘Found Family’ stuff which ends up being super popular in most LGBTQ+ media because we’re disowned by other people. (Data accepted and accepting himself as part of the crew, Worf and Alexander aren’t too awesome but Deanna steps up a bit there. You’ve got Wesley who’s kind of adopted by most of the upper ranks after a while.
-
TNG is purely “Infinite Diversity in Infinite Combinations” which people see as gay agenda because they wanna collapse anything pro-diversity as just being LGBTQ+ because they have fragile pathetic minds.
-
Q is aggressively queer coded. The hyper dramatic and flamboyant personality, the penchant for being a theatrical whore, openly flirting with Picard (and Riker) in such a way that you genuinely aren’t sure if he’s joking or not, he rejects every type of rigid norm from humanity, Voyager and a few other things even hinted in such a way that due to his ability to change form he’s above gendered norms too and sort of gender fluid. Not to mention being the campiest motherfucker this side of the Alpha quadrant. “It matters to me. YOU matter to me. Even Gods have favorites, Jean-Luc. You’ve always been one of mine.” There’s also his deep fucking loneliness, something that a metric fuckload of people in the community suffer from. Part of a whole but ostracized and on the outside? Yea.
“The Host” was another, and of course introducing the Trill species concept opens up for further things later on. The biggest flaw of that episode is how Beverly didn’t seem to consider a continued relationship after the new host ends up being female. Which is a fine reaction, but for the show pushing boundaries they could have at least had her ponder the idea even if she didn’t act on it. After all, who did she love? In that initial version of the Trill, the host was seemingly not in control, unlike later versions like Dax where the symbiote and host mix to create a shared personality.
I don’t think you need “sort of” for gender fluid. When you’re an omnipotent being of pure thought, you’re whatever gender you wish to express yourself as and you almost certainly express it as different genders for different situations on different planets and societies if you’re like Q and you want to spend eternity fucking with them.
I’d also say Odo was gender fluid. Or at least he’s a literal fluid with no gender unless he wishes to have one. He’s not expressing a gender when he’s in his bucket.