Our guess is Ninja Gaiden Dragon Sword, which just happens to be one of the best games of 2008. What a delight it would be to get it at one of the best prices of 2008! Other ninja-related games we can think of offhand include N+ (another honoree!), Ninjatown (wow, a lot of ninja games in our top 10), Tenchu: Dark Secret (not so great), various Naruto releases, the Izunas, Ninja Reflex, and Taito's Legend of Kage 2 -- which you can get for cheap right now.
[Update: it's Ninjatown for $20!]