The most well-known mascot for the transgendered is Ranma Saotome of Ranma 1/2. Ranma is a teenage martial arts expert who lives with a curse: when he is doused with cold water, he turns into a girl. Only a splash of hot water will make him revert to male form. The original manga by one of Japan's most popular cartoonists, Rumiko Takahashi, is played for laughs. Ranma 1/2 became a popular animated TV series and spawned several movies.
The English language Ramna 1/2 site.
Some YouTube links:
Dream balloon:YouTube - Ranma Music Video - Yume no Balloon
A character similar in predicament to Ranma is Shimeru Futaba of the manga Futaba-kun Change. Instead of water being the catalyst, emotion is what triggers the transformation. Futaba-kun changes into a girl whenever he gets excited. In the process of dealing with his newfound femme self, Futaba-kun manages to become a singing idol.
Another transgendered character is Aoi Futaba, policewoman in Kosuke Fujishima's Taiho Shichauzo (You're Under Arrest) manga and anime. Aoi-chan is actually a policeman who dressed as a woman for hazardous vice squad missions, trapping muggers and molesters. Over time, Aoi found he liked being a woman and has assumed the role permanently, even in her personal life. The other officers in the precinct are aware of Aoi-chan's situation and treat her every bit as a fellow policewoman. You're Under Arrest manga is published by Dark Horse Comics.
Also see this site for themes: Jana's TG Manga And Anime