Get The Sword- Press Left, Right (2 times), Up, X (2 times), Square at the main menu.
Invincibility- While the game is paused press L2, R2, L2 (3 times), R2 (3 times), Circle, Triangle, Square, Circle, Triangle, Square. If done correctly the ninja will turn into a skeleton and you will hear a chime. Just do the code again to change back.
Big Head Mode- As Press Start flashes at the title screen press Select, Select, Select, L2, L2, L2, Select, Select, Select.
Random Weapon- While the game is paused, press R2 (3 times), L2 (3 times), R2 (3 times),L2(6 times). Resume the game and you've got a new weapon. Repeat for multiple weapons.
Baby Ninja Mode- As Press Start flashes press L2 (3 times), select (3 times),R2 (3 times).
Less Boss Energy- While fighting a boss, pause the game and press L2 (3 times), R2 (3 times), Triangle (6 times) to weaken the bosses energy.