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Ninja of the Crescent Moon  - a mercenary clan whose members engage in sabotage and other covert missions for outlandish fees.  (from S&F) The Ninja's of the Crescent Moon are a mysterious organization, whispered about and feared in many circles.  Anyone of appropriate skills who manages to track the rumors and whispers back to their organization is usually offered membership.  Those who decline, or who do not have appropriate skills in the first place, are never heard from again....
Ninja Spy - One of the most enigmatic and mysterious of all classes, true ninja spies are masters of exotic weapons, tools of stealth, and strange ki powers.  (from Oriental Adventures) While some ninjas are little more than assassins (and may adopt that prestige class), a true ninja is more skilled. Additionally, ninjas are members of secretive clans (such as that of the Crescent Moon, which has its own version of prestige class; see above). 
The head of the clan holds absolute authority over the ninja's life and death.  Additionally, they are sword to secrecy to protect the identities of their clan members and must never reveal that they are ninja.  Despite an inclination to evil, ninja believe strongly in a code of honor, and risk offending their family (and earning death) if they break that code.
Like the Ninja of the Crescent Moon, anyone with the appropriate skills who manages to track down the rumours and whispers of a clan is either offered membership, or never heard from again...