Ninpuu Kamui Gaiden

Kamui is a ninja from the Edo period who has decided to leave his clan. After doing so he is pursued relentlessly by the members of his former clan; who consider him to be a traitor and therefore wish to kill him. Kamui then wanders around Japan to escape from them by using his intelligence and great abilities to survive. In the course of the series Kamui begins to suffer from paranoia because of his status as a persecuted man. Kamui then started to believe that everybody wished to murder him and became distrusting of everyone he came across. (Source: Wikipedia)

Ninja the Wonder Boy

Sasuke is the story of a ninja child that starts right after the battle of Sekigahara where Tokugawa Ieyasu becomes shogun of Japan. Sarutobi Sasuke (Jump Like Monkey Sasuke) was a famous ninja in the employ of Sanada Daisuke who fought for the losing side against Ieyasu. He was believed to have committed suicide when he was trapped in a castle, but the story takes off that he really escaped and that Sarutobi is not a name of a ninja but a whole ninja clan. (from AniDB)

Naruto

Naruto Uzumaki, a hyperactive and knuckle-headed ninja, lives in Konohagakure, the Hidden Leaf village. Moments prior to his birth, a huge demon known as the Kyuubi, the Nine-tailed Fox, attacked Konohagakure and wreaked havoc. In order to put an end to the Kyuubi's rampage, the leader of the village, the 4th Hokage, sacrificed his life and sealed the monstrous beast inside the newborn Naruto. Shunned because of the presence of the Kyuubi inside him, Naruto struggles to find his place in the village. He strives to become the Hokage of Konohagakure, and he meets many friends and foes along the way. (Source: MAL Rewrite)