My first ever story written online was gender change anime fanfiction, so this is a genre that holds a lot of interest for me, at least in some variations.
One of the most obvious facts about gender change stories it that, overwhelmingly, they are about turning from male to female. There are several reasons why this may be the case. One, there's a greater taboo factor. Women are encouraged to break some taboos surrounding their gender, but men are not given that same support. Men can still be ridiculed for wearing women's clothes, but there no longer is such as thing as "men's clothes." The taboo factor makes the change more dangerous and thus more exciting. It also encourages men who feel a desire to express their feminine side to sublimate those feelings, meaning seeking out a story online can be one of the only ways they connect with that part of themselves.
Another reason for the "gender gap" is that, as a society, we view women as the ideal in terms of beauty. Depending on your point of view, we glorify or objectify the feminine. This can make a feminine transformation seem more alluring.
Gender change transformation catalysts can include magic wishes, women's clothing, and - less commonly - the realistic process of hormones and surgery.
Gender change is one of the few transformation genres in which the physical transformation need not take center stage in the story. Often, the character wakes up having already been fully changed. Instead, a significant focus is often placed on how the character's life has changed, post transformation.
Like many other types of transformations, there's a divide within gender change stories between seeing the transformation as fortunate or as a punishment. In the "punishment" stories, the character often becomes a slut or a bimbo. Though they often have fun sexually, there's an undercurrent that being forced to be female is a humiliation. A similar genre is stories involving "forced feminization" or "sissification" in which the character is made to be more feminine but not actually turned into a girl - these stories also play on the association between humiliation and male femininity. I would love to see a "forced fem" story where being feminine is portrayed as a positive instead of a humiliation, so if you know of one, please share in the comments.
The "fortunate" stories usually leave their characters happier, better adjusted, more successful romantically, and closer to their "true" selves after the change. Kashimashi: Girl Meets Girl, the anime I recently reviewed, is a great example of this type of story. I tend to prefer the "fortunate" stories overall, though I'm always up for a dark story if its well written and the idea has some element of uniqueness.
If you're looking for a gender transformation story that places a lot of detail on the process of the change, Cheer is a great one. If you're looking for a story that places a lot of detail on the process and involves a rare female to male change, Sex Change Computer Virus would be my choice.
I'll be releasing a new ebook with a gender change theme during my next ebook release (I'm shooting for October 1st.) It actually falls under a sub genre, male to BBW, in which a man becomes a woman and gains weight. It was a blast to write.