As someone who used to be the manga expert for a local Borders...this thread made me very happy!!!!!!!!!!! In fact, there's only one place to sit in my apartment because everything else is covered in manga.
Here are the ones I like (there are some repeats) for this particular topic (keep in mind that they are fiction stories and things rarely work out this well) (if I were at home the list would probably be much longer...but I can't remember everything)
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Day of Revolution-
Angel Sanctuary (WARNING...it's a love story between a brother and a sister, so if you can't get past the incest, don't read it...That being said, it's one of my favorite manga ever and Kaori Yuki is an amazing artist)
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Until the Full Moon-
Gentleman's Alliance (there's a boy who crossdresses)
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Kashimashi-
Kedamono Damono-
IS (NOT the Shonen Jump IS)--It is about people who are intersexed...you can download it from The Evil Empire...I think it's in the yaoi section.
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Fushigi Yuugi (though Yuu Watase isn't for everyone...this one is particularly dramatic...and long...but Nuriko is my favorite character!)
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Ouran High School Host Club--I mention this one because the main character is female, but even in the beginning she mentions (she's a commoner at a rich school) that she doesn't really appreciate the perceived differences between the sexes...she wore old hand-me-downs and they thought she was a boy...mostly, it's a silly story, but the main character is not your typical 'japanese school girl' heroine...in fact, anti-heroine is probably the best way to describe her.
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Yellow -
Gravitation and
Gravitation EX Yoshiki is a transexual
Another good website is
www.animecornerstore.com. You can order just about any manga/anime that's currently in print from them.
Those are the only ones that I could think of (off the top of my head) that deal specifically with gender-bending issues (not just crossdressing for love/money...that happens a lot too)...however, relationships in yaoi (boys love) manga are often 'based' on the fact that a person can fall in love with anybody, regardless of gender...well, I say 'based', but mostly it's just that their characters aren't always gay, they just happen to fall in love with men...it's a plot device...when there is a plot...there's a lot of smut too...what does that say about me? >
I do think that manga artists push the envelope, but then again, they are still restricted by what is culturally acceptable in Japan. In most yaoi, the main characters almost always mention that they date women too, so they aren't gay, they just happen to like some men. I guess that makes it okay...

Maybe I'll think of more when I go back home...If anyone has any questions about manga, whether it be suggestions or appropriateness for kids, etc, feel free to contact me!