Currently, there are two non-MK games that feature MK characters as far as I know.

The first is The Grid, an arcade only multiplayer deathmatch title.  It's fast, it's funny, and it's unbalanced, but it's a whole lot of fun.  Scorpion, Sub-Zero and Noob Saibot are all hidden playable playable characters.

The other game is Unreal Championship 2: The Liandri Conflict (official site), which features Raiden is a playable character.