In my never-ending quest to find good manga, I found a manga/comic essay called 僕が私になるために (Boku ga Watashi ni naru tame ni - For me to become me), by Hirasawa Yuuna. It is an autobiographical story about the author's journey from man to woman. It's very educational, and gives a serious, but still funny insight into the transition process (mainly the actual surgery).
If you're transgender, or simply interested, and happen to know Japanese, I'd suggest giving it a read. Hopefully some scanlation group eventually picks it up so more people can read it (I have too many other projects I'm interested in...).