Check out Lone Wolf & Cub, Samurai Executioner, and Lady Snowblood which are all written by Kazuo Koike.
I think you will also enjoy Usagi Yojimbo by Stan Sakai, an excellent anthropomorphic historical fiction/fantasy series.
You might also like Blade of the Immortal, and the upcoming Satsuma Gishiden.
All the above titles are published by Darkhorse.
I would also recommend the novels Taiko, written by Eiji Yoshikawa, (The author of the Musashi novels upon which the manga illustarted by Takehiko Inoue is based.) Cloud of Sparrows, and Autumn Bridge, by Takashi Matsuoka.
