Level Select:

Hold Select + Square + Circle and press Right(3), Up, Left, Down, R2 at the level selection screen. Note: More levels will become available if Tatsumaru has already been unlocked as a selectable character. Alternately, press Start at the map screen and enter the load/save menu. Then, hold R1 and press Up, Down, Square, Up, Down, Square, Up, Down, Square, Down, Up, X.

Recharge Health:

Pause game, press and hold Square, then press buttons Left, Right, Up, Down.

All Missions in Mission Editor:

Enter the custom mission screen in the mission editor, then hold R2 + Circle and press Up, Down, Down, Right, Left, Left.

Game Levels in Mission Editor:

Enter the mission settings screen in the mission editor, then hold Circle and press Up, Up, Down, Down, Left, Right.

Unlock All Ninja Items From the Item Selection Screen:

Press Square(3x), Circle, Square, Circle, Circle, Left, Up, Down, Right, R2, R2.

Increase Item Inventory by 1 From the Item Selection Screen:

Hold R1 and Square and press Right, Down, Left, Up.

Play as Tatsumaru:

Beat the game as both Rikimaru and Ayame. Or You'll be able to use Tatsumaru in the mission editor after inputting the following code from the Stage Selection screen: Hold Circle and Square, press R1, R2, L2, L1, Up, Down, Left, Right, and Select.

More Objects & Tilesets for Mission Editor:

Simply advance further in the game to make new areas and object available in the Mission Editor.

We're Not in Japan Anymore:

Beat the game with all three characters and then go to the mission editor screen. You'll notice a European castle to play with, complete with knights and nobles.

Full Map of the Level:

While playing the game, hit select to display the map, then press Circle, Circle, Circle, Circle.
Note: Once you let go of select, the map will clear. You will have to put in the code again to see the full map.

Interesting Looking Rikimoru:

At the item select screen, use "ninja armor" and when your done picking and have entered the game he will be.

Rotate Objects:

When using the mission editor, hold R1and press Circle to rotate objects such as bridges and roofs.

Shark in Last Level:

During the last level, go to where you fight the first boss. Go around his ship to the right side (coming from the south side) and swim in the water north/northeast to find a very big ship that towers above anything your grappling hook can even touch. Swim around on this side of the ship for a while. Somewhere nearby a shark should appear in the water. The shark will put the enemies on alert as if he was a normal enemy.

Put Away Your Weapon:

Quickly press Circle twice.

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 weapon will be drawn out, and you will perform a stealth kill.

Drag Away Your Enemies:

This doesn't usually work on bosses. After killing an enemy, simply go near them and press R1 + O then press the directional button. Now you can drag these losers away and drop them like in the water or something.

Pick Up Dropped Items:

This cheat works best after a stealth kill or an undetected kill. After which, just go near their dead body and press R1 + square. You will eventually get an item or two.