I would like a gender bender with a smart female lead. Preferably relatively calm and mysterious. And when I mean smart, I mean clever and/or perceptive; high grades are not required. Please no dense heroines.

It can be any genre, but I'd like the girl to have a serious reason for cross dressing (or even becoming a trans), and to have an air of mysteriousness. Basically, she can't be dumb.

Also, even though I'd like some romance, I don't mind it in hints or as a subplot. (It can even be semi non-existent---I have a good imagination.) And the girl can be a lesbian (and I mean a real lesbian please, none of this, "Oh, I suddenly like guys!" business).

Shoujo is a waste of time that makes me happy.

Go to Farhad's forum.
http://tgmangas.xeraweb.com/forum/
They'll be able to help you more than anyone else here. Careful though, they post a lot of adult content.

Is this me in a nutshell?
Pretty much.
[img]http://www.dragonflycave.com/wpay/ninetales.gif[/img]

I'm not too sure, but after a quick search, how about ...

• Love Sick
• Hana no Kishi
• or maybe Gekkou Teien? ^^"

"It's like love is a bonus in your life. Even without it, I'm just fine. I don't feel like pointlessly searching for it. You don't have to make yourself unhappy." (Ookami Shoujo to Kuro Ouji)

"Why does it rain?" - "To create drama." (Drops (Andou Yuki))

Wandering Son has two protagonists one is a boy and the other is a girl, they claim to both be transgender. It's a serious manga and goes at a level pace which takes transgender and LGBT issues realistically. Yoshino, the girl, is an outwardly cool character who is more observant than most people.

Penguin Kakumei - very calm female lead, smart too.

Bokura no Kiseki - I've only read a chapter or two, but it fits as far as I've seen.

I can only think of Basara by Yumi Tamura, which fulfills your criteria of cross-dressing female (for good reason) who is smart, brave, and strong, and not annoying, weak, or is a crybaby. Looking at your other forum posts, it also fulfills your criteria of black-haired female MC being end up with black-haired male.
It is a historical and action manga though and is a long series, but with real plots and good character development. I think it is one of the better shoujo/josei manga.
Hope that helps.

Savage garden
The heroine wasn't dense or too smart. I think she was normal, and she is different form cliche shoujo heroines, and likeable^^ Doesn't fall in love so easily and has an actual reason to pretend to be a boy...
And also i second Bokura no Kiseki^^ (Though the main character is a boy- not a girl- well, it can change from the point of view.)

Savage Garden --> Sappy, dramatic, with really horrible rushed ending, IMHO. But the art is beautiful though.
Bokura no Kiseki --> Looks interesting. I woulldn't mind reading something like that. I'm adding that to my future reading list 😁

Saver