Your and My Secret Volume 1 by Ai Morinaga (amazon)

Your & My Secret is the craziest gender-bending manga I have ever read. Granted, I have not investigated the genre throughly, but it seems like it would be very hard to top this book. I can see now why people were so excited when Tokyopop picked up the license for this manga after ADV dropped it!
Akira is a cute guy, but he has an extremely dull personality. He’s very shy and passive, so people generally tend to walk all over him, or ignore him as a non-entity. Akira has a crush on Nanako, who is a cute girl, but she’s extremely abrasive and aggressive, to the point where most of her classmates are afraid of her. Thanks to a scientific experiment gone awry, Nanako and Akira switch bodies.
Nanako delights in her new male body, seizing the opportunity to slam dunk and sign up for karate. When Nanako’s best friend Shiina is sick during P.E., she picks her up and carries her to the nurse’s office. The result of the personality switch is that everyone is impressed with the new and improved Akira, and Shiina quickly develops a crush on him, not knowing that her female friend Nanako is inhabiting his body.
In the meantime, Akira struggles with inhabiting the body of the girl he has a crush on, dealing with changing in locker rooms, and cleaning up her pigsty of a room. Akira’s best friend Senbongi starts to notice the new, shyer Nanako and wonders why she suddenly seems more cute. Akira thinks that he’s turning more girly the longer he stays in Nanako’s body. Soon, Nanako decides to start dating Shina while Senbongi is making passes at Akira.
Most of the humor in the book is found in Nanako’s matter-of-fact acceptance of the shift, combined with Akira’s dismay at the female-centric situations he finds himself in. He thinks that Nanako is a better man than he is, as she quickly ingratiates herself with his family and turns into a very popular boy at school. Your & My Secret effectively satirizes the traditional gender roles found in shoujo manga.
Morninga’s art is attractive, and she easily captures the shift in body language and facial expressions that occurs when Akira and Nanako switch bodies. My only quibble with this manga is that since it is told mainly from Akira’s point of view, we don’t really see any of Nanako’s thoughts and it would have been interesting to see more of her internal emotions as she adjusts to a boy’s body. But then, Akira’s reactions to her probably wouldn’t be quite as funny.