First of all, the best and most complete list I have found compiling all relevant or possibly relevant trans-adjacent manga is given by @hdittus13 on twitter, in this Google doc. It is important, however, to note that manga as a whole is largely afflicted with many misconceptions surrounding transpeople and the LGBTQIA+ community, and as a result most manga showing representation of trans and nonbinary people are highly flawed even when intentions are admirable.
Thus it becomes necessary to filter through these manga looking for representation that contains as little fetishism as possible, represents real struggles and at the very least refuses to represent entire lives as simply a 'phase' prior to the repressive Karoushi breeder lifestyle. These reviews will hopefully help you in this process. The following criteria (which I shall explain later) I see as indicative of a trans-adjacent manga being a kind of 'Holy Grail':
Note: I will likely be focusing largely on transfeminine characters on this page as I am a trans woman.
Here is a quick list of my personal favourites without factoring in accuracy of representation. Actual categorising of such manga will come later.
First, note that one cannot expect any element of a medical transition process to be noted by ANY mangaka who is not themselves a transperson. Excepting the few manga which are written as autobiographical accounts from trans mangaka, it is absurdly rare to find a manga which mentions medical transition as even a possibility. Sometimes the mindset on display here is that 'crossdressing' is an activity of youth, but once youth is over, then there is a fundamental 'impossibility' of passing. However, this is not always the case; even very explicitly pro-LGBTQIA+ manga will show gender dysphoria in children and completed transitions only. It is almost appears to be a taboo to show how any such completed transition was accomplished - one almost never encounters surgery, let alone HRT. Part of me wonders if this is something to do with Japan's prohibitive drug laws and perhaps the demographics of the manga in question, but looking at drug use in edgier shounen anime immediately shows that any failure to do so on the part of mangaka cannot be explained this way.
Aside from these autobiographical manga, likely the most comprehensive manga I have read in this regard is the romance '"Onna" toshite Idakaretai...Seitenkan Shite, Hatsukoi o Mou Ichido', which speaks of the trans woman protagonist's HRT and sexual reassignment surgery. Unfortunately however as of 11th July 2022, I have not encountered any other non-hentai manga which even mentions surgery as a possiblity. Moreover, from what I recall the only other manga even implying HRT is Stop!! Hibari-kun! in a bonus chapter released long after the series had ended (a trans boy is seen injecting testosterone). Finally, Bokura no Hentai deserves an honorable mention for even showing one of its protagonists visiting a doctor in order to be assessed for gender dysphoria - this assessment, however, is purely to convince her school to allow her to wear the girls' uniform.
Although most manga featuring trans and nonbinary characters are often blatantly misguided and prejudiced, there are some which can be rehabilitated if certain aspects are ignored. The best, and perhaps first example of this must be Stop!! Hibari-kun!, which often got so much correct for a 1980s shounen manga that it is hard to dismiss outright. The most crucial aspect of this comedy is that the trans girl deuteragonist, Hibari, is NEVER the butt of the joke; it is almost always the case instead that those who attempt to out her as trans and/or are angered by the fact that she passes attain comeuppance as a result. Often it is Hibari herself who is actively taking charge - on more than one occasion when the protagonist attempts to out her in public she will violently silence him.
There are points at which it truly appears as if the mangaka was intending to gradually have Hibari be seen as valid for who she is, especially with relation to Hibari's implied gender dysphoria with respect to breast growth. It is a shame however, that the mangaka largely lost steam, introduced new characters, went backwards on actual acceptance of Hibari by her sisters, and constantly teases the reader that the protagonist is slowly falling for Hibari in spite of his transphobia (and due to Japanese culture's lack of distinction between homosexual men and trans women , he de facto exhibits homophobia in his assumptions and insults that she is simply a homosexual man). Despite the bonus chapter, Stop!! Hibari-kun! is largely unfinished, and due to the mangaka's erratic work schedule later chapters are often marred by cutaway gags featuring the author refusing to draw more. It is notable also that later chapters on a few occasions feature racist visual jokes. Overall, it is unfortunate that this manga had incredible potential that was squandered by indecision and meandering backtracking. To this day, however, the art is superb and it is worth reading for this alone.