Yes, so as the title suggests, I am looking for manga that includes Bifauxnen (female who are mistaken for bishie males), but I am not limiting it to that.
I am also interested in any FtM transgender, androgynous, genderqueer...simply mysterious and up-in-the-air gender mixups.
They don't need to be the lead, they don't even have to be secondary, they could be the villain and I would not care, to be honest. The reason also doesn't matter to me. Whether they dress that way because they feel most comfortable, or they do it to achieve a specific goal (get into gender-exclusive schools, for example). They also do not have to be female mistaken for male. A male mistaken for a female masquerading as a male pretending to etc etc, or any other Victor Victoria-esc situations suit me fine.
Also, it is not relevant whether the image is maintained throughout the whole manga, whether he/she is found out, or if people react positively or negatively to said person.

I don't want the gender-bender kind where a male character is turned female for some reason and now has to cope with it.
I also don't want things like boys in giant puffy loli dresses, where it is used as...say a yaoi fetish or something.

That being said, I am not adverse to suggestions that fall under the yaoi/yuri/ecchi/rape banner, as long as that is not 90% of the manga (I am asexual. And while very neutral to sex, there is only so much mindless lecherous content I can take before I am bored by it)

Examples of such, which I have already read:
Wandering Son
Himegami
Ouran HSHC
Minami-ke
Kurau Phantom Memory (admittedly, this is anime not manga XD')
Kaze Hikaru
Yotsuba&!
+Anima
Tokyo Crazy Paradise
Family Compo
Nononono
Princess Knight
Penguin Revolution

try these for gender blender, i tried to pick one that seemed like they had the most posts

http://www.mangaupdates.com/showtopic.php?tid=2257&hl= gender blender
http://www.mangaupdates.com/showtopic.php?tid=3916&hl= gender blender
http://www.mangaupdates.com/showtopic.php?tid=2017&hl= gender blender

personally, i enjoy
hana no kishi
nosatsu junkie
saver
never give up!
fantamir
angel diary
and a ton of others i just can't recall.

edit:
omg, i totally forgot about
my boyfriend is a vampire
and you should check out HAN Yu-Rang and HWANG Mi Ri. about half the stuff they have is gender blender. as for the other genres, i'm not interested in them so i don't have recommendations for them

Savage Garden

girl dresses up as a guy to attend this all boys school in the place of her friend Jeremy, who is dead. she is definitely seen as a bishie male, and since this is an all boy's school, you can't be squeamish witth shounen-ai stuff.

1/2 Prince

girl buys this alternate reality fantasy game, but in it she makes her character a guy (you aren't supposed to be able to do this). soon she becomes really famous and popular in the game, but only a few people know that she's not actually a guy. definitely bishie.

Maria+Holic

girl enters an all girl's school in the hopes of finding her true love. she's really attracted to her roomate . . . until she finds out that she's actually a he. and not only is he a guy, he's also very sadistic. however, he only acts that way around her . . . everyone else thinks he's a perfectly angelic girl.

Kimi to Himitsu no Hanazono

girl who is often mistaken for a guy enters this school to learn to be more ladylike, but her roommate, the perfect example of a lady, is actually a guy. this one's fun, because when they're together, he looks like a she and she looks like a he

Gentlemen's Alliance Cross

girl joins this prestigious school and becomes a member of the student council (she's trying to win her love's heart). one of her friends on the student council is actually a cross-dresser (you'll have to figure out which one, because they don't tell you at first) who has feelings for her and this other guy simultaneously

Hope this helps some

Try the Manly/Handsome Female and Trap tags.

As well as TvTropes if you haven't already.

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Ai wo Utau Yori Ore ni Oborero!: The male and female looks are switched (The girl is brutally handsome, guy is terminally pretty). The guy does dress up in girly dresses some of the time, although it's not because he likes to, he does so to hide his identity. Several of the female lead's friends are Bifauxnen as well.

Off the top of my head, what I can think of are these:

Butterfly - mainly supernatural, with little to no romance, but the story doesn't center around the gender-messup.

Id - the main protagonist is always mistaken for a girl. However, the story also does not center around that concept. It's mainly about a person who calls himself Id who goes to another world and his adventures there. My summary doesn't do it justice. You'll have to read it for yourself. There's a lot of gender puns and jokes.

Prunus Girl - this one is a guy who looks exactly like a girl, acts like a girl, but is actually a guy. He feels most comfortable dressing as a girl. Is also romance. However, it's not really shounen-ai.

Romeo x Juliet - it's not like Shakespeare's Romeo and Juliet, but it's a twist on it. The Montague family has taken over and is oppressing the citizens of Neo-Verona, and Juliet is the only daughter of the deceased Capulet family, thus making her the leader of the uprising. Romeo is the son of the Montague family. You know the story, except that Juliet has to dress up as a guy sometimes in order for people not to know that she's the living daughter of the Capulet Family.


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