Let's face it,ninjas were HOT in the 80s. You got whiteboy american ninjas,ninjas kidnapping the President,mutated teenage turtle ninjas,scarf-wearing 2D ninjas and generally a lot of guys in pantsuits. Since ninjas have covered such an array of media,it's best if you name your favorites by genre:
1) Movies
Sho Kosugi

http://www.youtube.com/watch?v=E3xLaBYnShU
Kosugi-san is the embodiement of awesome. He actually is an accomplished ninjutsu master and his movies -specially Revenge of the Ninja and Pray for Death- epitomized everything that was godly about ninjas back in the day. He'll be appearing in the upcoming Wachowski brothers flick,Ninja Assassin.
2) Comics/Animation
Storm Shadow


C'mon,does this one requires explanation?
3) Videogames
Joe Musashi (Shinobi)

Y'know,even with all the great videogame ninjas that have come over the years the one that retains that Sho Kosugi-like level of ninja-ness is still old Joe. Too bad most people remember this series for the inferior home console ports and not the awesome arcade game (still waiting for that XBLA port,Sega!)

Honorable Mention: Scorpion
