Alternate selection screen
At the Konami logo before the introduction to the game, press Start in order to get a different picture at the selection screen. Instead of a pictures of the Ninja, it will feature the Ninja with his mask broken open.
Special mode unlocked
While playing any level on sneaking mode pause the game and hold L1 and press L2, R2, Triangle and R1. Then Unpause the game and keep repeating until you hear Snake say something. Then go to special mode and everything will be unlocked!