All Ninja items 

At the item selection screen, press Square(3), Circle, Square, Circle(2), Left, Up, Down, Right, R2(2).
Submitted by U-God

More inventory space 

At the item selection screen, hold R1 + Square and press Right, Down, Left, Up.
Submitted by U-God 

Full map 

While playing a game, hold Select to display the map, then press Circle(5)
Submitted by U-God .

All missions in mission editor 

Enter the custom mission screen in the mission editor, then hold R2 + Circle and press Up, Down(2), Right, Left(2).
Submitted by U-God 

Game levels in mission editor 

Enter the mission settings screen in the mission editor, then hold Circle and press Up(2), Down(2), Left, Right.
Submitted by U-God 

Office tileset in mission editor 

Enter the edit mission screen in the mission editor, then highlight the "New Mission" selection. Hold L2 and press Circle, Square, Left, Right, Circle, Square. If you entered the code correctly, you will hear a sound.
Submitted by U-God 

More options in mission editor 

Simply advance in the game to get more options in the mission editor. As your character reaches new levels with new tilesets, the same tileset will then be available in the editor.
Submitted by U-God 

Play as Tatsumaru 

Successfully complete the game with both Rikimaru and Ayame.
Submitted by U-God

Hints 
High jump 

If you are in certain levels (Quarantine Village, Laborers), you do not need a grappling hook to get on to the roof of a house. Run up to the wall, face it, and jump. Your character will jump twice the normal height of the usual jump and land on top of the roof without hanging on the side.
Submitted by U-God 

Easy kills 

Hit an enemy who is not aware of your presence in the head with a blow gun dart to automatically kill them.
Submitted by U-God 

Automatic stealth kill 

You do not need to pull out your weapons to perform a stealth kill. Run to the enemy and press Attack. Your weapons will instantaneously be drawn out, and you will perform the stealth kill.
Submitted by U-God 

Stealth kills 

You can get the different stealth kills by being in the correct position in relation to the enemy.
Submitted by U-God 

Easy stealth kills 

Sneak up from behind.

Sneak up from behind and crouch.

Jump on enemy, while pressing Attack in mid-air.
Submitted by U-God 

Moderate stealth kills 

Sneak from the side.

Hard stealth kills 

Sneak from front (or wait for them to turn around into you). Note: This must be timed perfectly.