Woo, I didn't know that there were samurais who were familiar with ninjutsu. I learned something today.
Ninjas were basically spies. From my understanding, they did fight/kill occasionally, but mostly carried out espionage related activities. Also, their costumes consisted of peasants, or farmers clothes, and not those ultra slick black nenjya(that's how my American friends pronounce it for fun) suits, most of the time. They did have to blend in.
Diablomonkey's right about samurais focusing a lot on their code of honor(at least the good ones), where ninjas, if they cared about honor, they'd be dead ninjas. But as Speedy said, that's not what separates ninjas and samurais.
This is the weirdest birthday thread, ever. I'm so proud....