I debated on this one for a little while; it's not a comic, and it's not particularly transgender. However, it is available on YouTube and it shows a different culture of cross-gender thoughts, so it's actually a perfect fit for the column.
Ouran High School Host Club follows Haruhi's adventures as an unwilling, stealthy member of the Host Club, a group dedicated to throwing elaborate parties to entertain rich women. Unwilling, because she is paying back a debt; and stealthy, because she's a girl dressed as a boy.
What unfolds, for better or worse, is mostly typical of anime aimed at Japanese girls. There is a love interest between the leader of the Host Club and Haruhi. Sparkles and highlights litter the edge of the screen while women swoon and cheer. Chauvinistic romance is planned and played out for these parties, as the hosts attempt to woo women like princesses. Because it's an episodic anime, episodes often follow a predictable path: Host Club plans a party, Host Club encounters problem, Host Club fixes problem, Host Club has a great party.
The anime is unique insofar as it makes fun of traditional romantic stereotypes. Haruhi, unlike her foil Tamaki, is a calm, well-reasoned woman who doesn't subscribe to the pretty-princess school of the feminine arts. She is comfortable presenting as a male - partially due to her familiarity with crossdressers vis-à-vis her father - and carries herself with intelligence and grace that the Host Club members find admirable. There is a romantic interest, but the role of stoic, masculine indifference goes to Haruhi, not Tamaki.
Overall, I'm very impressed with this anime. It's cute, fun, flirty, and yet it carries a certain vein of counterculture that saves it from the fate of other forgettable romance cartoons. It's not for everyone, but definitely worth seeing an episode or two at the very least.