Hattori Hanzo, Eiji Kisaragi, Zantetsu.

Shadow Man from Mega Man 3.

I'm gunna' throw in Sasuke from the Goemon games.

Does Deadpool count? He claims to be a ninja at least.

http://www.youtube.com/watch?v=Are2uSLBRs0

That is a tough one.

Ryu Hayabusa from Ninja Gaiden. No ninja has made me want to bitch slap a dog more than him.

I'm partial to Ayame from the Tenchu series, I love her fighting style and stealth kills, although Rikimaru is great as well.

First off all: That beautiful red guy in my avatar, lmao. I don't care if people say he isn't a ninja - he's more of a ninja than that Naruto twat ever is!

Ryu Hayabusa: He's too badly nerfed in the Dead or Alive games though :)

Tenchu Series: Tatsumaru> Rikkimaru> Ayame :D

Joe Mushashi

Taki

Ninja Fu Hiya (I pity those who do not know where he's from, lol)

WHAT!! NO BATMAN!! Shame on you!!

LOL
I hate these little bastards! :P .........
.......

<_<

>_>

I never played Ninja Gaiden.

I didn't liked playing with Ayame in Tenchu 2. Rikimaru was much easier to control, so I always played with he.
But the devs improved her control immensely in Wrath of Heaven. In fact, I prefer to play with her in that game.

Strider Hiryu is cool. I liked playing with he in Marvel vs. Capcom.