Actually... and this is according to 2nd edition D&D rules, it may have changed in 3rd...
Ninjas were never their own class, nor were they really a thief class. Part of being an effective ninja was never having anyone know that you were one. Ninjas actually were required to multi-class with another oriental class character (wu-jen, kensai, etc) to help conceal their identity. Ninjas had some nice bonuses granted to them, like immunity to poison after a certain level, the ability to run across water for x amount of feet per lvl, the ability to fall x amount of feet per lvl without sustaining damage, pole vault x feet/lvl, and various other bonuses I can't remember. They only got 1-2 HP per lvl which blows but... hey, they're stealth, not rugged. They had a lot of ninja-only items that helped them do stuff easier, quicker, and quieter (sp?) than a thief. Smoke bombs, climbing tools, lotsa other stuff that escapes me right now... Tho I think they used the thief THACO and XP charts, they're really a seperate class. Oddly, the benefits aren't THAT great, but they're really fun to play when you have to constantly pretend that you're something else... tho people eventually get suspicious when the mage of the party is jumping in and out of trees and off walls like a chimp on crack.
Oh, and I think they had to be human. Yeah, I know, a multi classed human? Yes, a multi classed human alright... just so long as no one else finds out.
n-n-n-ninja!