Not exactly martial arts, but Zetman might interest you. Highly physical fighting manga, that has a lot of potential.

Another one is sword fighting, but I thought it was very high quality. A lot of potential here also. XBlade

Teppuu is a new manga that got me interested.

can't remember the best martial arts one but I thought vagabond was great for sword fighting.

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Realistic:
Kenji, mostly about chinese martial arts. The protagonists main style is Bajiquan.
Yawara！, about a cute high school girl who does Judo.

Historical:
Vagabond, about a famous samurai Miyamoto Musashi.
Sōten no Kōmori, beautiful one shot about a young shinobi (kunoichi) who wants to stop killing people.
Getsu Mei Seiki - Sayonara Shinsengumi, about Hijikata Toshizō, deputy leader of Shinsengumi.
Basilisk: Kōga Ninpō-chō, a fight between two ninja clans Kōga and Iga.
Hanzō no Mon, about a famous shinobi/samurai Hattori Hanzō.
Kurogane, Jintetsu's life is saved and given a steel body.
Dangu, Shaman Warrior.

Psychological:
Shamo, top student kills his parents and learns Karate in prison. Dark and psychological side of martial arts.
Holyland, high school boy who's sick of being bullied.

Sports:
Bamboo Blade, high school kendo club.
Karate Shoukoushi Kohinata Minoru, Kohinata Minoru former gymnast joins the second Karate club.
Bamboo Blade, high school kendo club.
Hajime no Ippo, the boxing manga.
Katsu！, a boxing manga by Adachi.
SUGAR, a boxing manga.

Action:
Aiki, not your usual action/ecchi martial arts manga.
Kenka Shoubai, too hard to explain in few words, check it out.
B・Reaction！, it's not long enough be too bad to be read.
Ultra Red, typical shounen/action martial arts manga, just a bit better and without ecchi.
Densetsu no Kashira Shō, and another one, only totally different.
Wild School, but not ecchi.

Comedy:
Dōshirō de Gozaru, a Japanese high school student first time in Japan, and his mind seems to still be in Edo era.
Ningen Kyōki Katsuo, either you like it, or you don't.
Noritaka, by the same author as the last one.

My personal top 5:
Kenji
Katsu！
Vagabond
Sōten no Kōmori
Getsu Mei Seiki
Yawara！

umm... 6?

Far-off places with sweet sounding names.

holy land and hajime no ippo are definitely great reads. I wish Illuminati would start again =D

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