* The arcade game ending. After you beat the final boss, Ryu is suddenly napping in a boat being driven by Muramasa, heading towards Japan. The skyline contains every one of Japan's most well-known landmarks, including Mt. Fuji and Tokyo Tower, [[ArtisticLicenseGeography which are miles upon miles apart in real life.]]
* The infamous [[http://www.youtube.com/watch?v=xbcMI0FjlBg Japanese Commercial for Ninja Gaiden Sigma 2]] that made the JigglePhysics controllability feature famous.
* In the Xbox game, Ryu's outraged expression upon interacting with a badly repaired window in Chapter 3.
--> '''Ryu''': What a careless repair job! Are they trying to make fun of Ninjas?