I'm not a really big ninja fan, but zorhau asked in a comment on my old class system post "What about ninjas?" So I'll give some thoughts on ninja characters.
I've complained before about turning professions into classes. I prefer keeping the classes more archetypal, although the flavor of their abilities can certainly be adjusted to make them better suited to a particular profession. So, a samurai is a fighter who acts a specific way and prefers certain weapons and armor; there's not much need to distinguish a samurai as a class. Similarly, the ninja as spy/assassin is a profession; you could use a couple different classes as-is for different kinds of ninja:
- ninja spy: a thief, or in my case the Trickster. The ability to use distractions in the middle of combat to re-roll surprise, combined with the ability to add their HD bonus as damage on a surprise attack, makes them pretty formidable. They just need to buy some flash-powder bombs and some disguises and off they go.
- ninja warrior/assassin: a hybrid fighter/trickster. He can't re-roll surprise, but he does get to add his HD bonus to damage on his first attack, if he gains surprise, and he gets the stealth and disguise abilities of the trickster, combined with the fighter's ability to use ANY weapon, even improvised ones.
- supernatural ninja: an Illusionist or hybrid Fighter/Illusionist. Weapons plus magical tricks. For a different take, use the Illusionist spell list, but make the class hybrid Fighter/Saint, dealing with spirits of deception.
(Those of you looking for a more thematically-appropriate class for the holidays might want to consider pilgrim Witch Hunters.)