I'm transfemme so most of the media I'm aware of is also transfemme, but I think most stories of transition offer useful perspectives regardless of what direction they're going. Here's some of the ones I know about.
For webcomics, there's three in particular that I connect to exploring my own transition. I Want to Be a Cute Anime Girl (first comic here) is a little cheesy but it is a comic entirely about someone's transition right from the moment she realizes she might want one. The other two are both comics that ran for a long time before the authors realized they were trans, and decided to introduce storylines about transitioning in their comics. The more detailed one is Real Life Comics (transition story starting here), the cuter one is Pepsiaphobia (transition story starting here).
But, I'm more familiar with video games than I am with webcomics, although most queer/trans games seem to be visual novels. In terms of those, GENDERWRECKED is a bit dark/silly but might be more useful to those exploring nonbinary identities. We Know the Devil and its quasi-sequel Heaven Will Be Mine are abstract, and aren't specifically about being trans so much as they're about being queer in general, but they are fantastic works of art with a lot to say about the complexities of life and relationships that I think would be useful to any trans person.
For a while I also made a point of collecting suggestions for games that are about being trans. Unfortunately I haven't played the following ones myself, so I can't vouch for their relevance or authenticity, but just so you're aware of them I have been recommended Secret Little Haven, One Night, Hot Springs, If Found..., A Normal Lost Phone, and Get in the Car, Loser!
If you are interested in additional trans experiences, I can also recommend ME, I can recommend MY BLOG,
