Quote from AnimeMusicLuv

HANA KIMI!!=D~ Yu gotta see this one,its awesome,funny as hell and very romantic=D

GO SANO!!

First of all, Hana Kimi sucks. Secondly, it doesn't fit what our TP is looking for from a gender bender. In fact, the main character of Hana Kimi does a HORRIBLE job of switching genders.

This signature was recovered from Hades to serve in my rotting armies.

true hana kimi isn't the type the poster asked for but let's try not to just throw the "it sucked" card around...

also as a recomendation, seeing as everybody already posted all the best ones i could think of, some series i'm not sure you'll like but vaguely fit your bill
my two wings beyond eechi, but some gender confusion
futaba-kun change a gender swap story, shounen, but funny and some romantic confusion later on
Yubisaki Milk Tea (closed match-ish) cross dressing/romantic confusion. personally love it

I.S. is like SUPER good in that range of topics!!! its amazing....

it seem some others have already said it but I totally support it....it is awesome...