umm..i think He's Dedicated to Roses, Boy of the Female Wolf, Love in the Mask, Zippy Ziggy, She's Scary, Why Do You Love Me?, Delinquent Cinderella, Oresama Teacher, and Hana ni Aeashi are a good ones..everyone else has mentioned the other one's I've thought of.
Obaka-chan Koigatariki might fit in too.
Ways of the Jogang Jicheo is kinda like that..there's only a few chapters, but it seems really good so far. 😎

7 seeds - Hana. She's not only a tomboy, she's an asset because of her physical skills.
Special A seconded!

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Image from Gangsta -> Full Image Link http://www.k4.dion.ne.jp/~babyrock/page030.html

umm, 3 Years, though it's only 3 chapters long, i found it really good for it's short length. The girl kind of stays a tomboy until the end, so i think it's okay. Anyway, you should try it out, i think you'll like it 😛

[img]http://img267.imageshack.us/img267/4466/princesswallpaper2560x1.jpg[/img]

"In a world where most people would be crazy, then it would be normal to be crazy and crazy to be normal... but then again, if you were normal, then you would be crazy... isn't it crazy what a paradox a little craziness can create?"

Shitsurakuen
Claymore

Otomen
Miss Modern
20th Century Boy
Angel Densetsu?
Maybe Gokusen fits too
Paros no Ken, well she wants to become male, it has shoujo ai if you don't mind
9 Banme no Musashi

Gokusen seconded. Also, Oresama Teacher.

Blooming
Vanilla Ice
Hush
W Juliet

Nulla in mundo pax sincera
"Always go too far, because that's where you'll find the truth." - Albert Camus