U.S. version codes: 

Level select:
     At  the  level  select  screen, hold Select + Square + Circle and
press Right, Right, Right, Up, Left, Down, R2.

Unlock All Ninja Items:
     At  item  selection screen, press Square, Square, Square, Circle,
Square, Circle, Circle, Left, Up, Down, Right, R2, R2.

Increase Item Inventory by 1:
     At  item  selection  screen,  hold R1 and Square and press Right,
Down, Left, Up.

Show Entire Map:
     During  the  game,  hold select to view the map and press Circle,
Circle, Circle, Circle, Circle.

Regain health:
     Pause the game, hold Square and press Left, Right, Up, Down.

Play as Tatsumaru:
     The hard way: Beat the game with both Rikimaru and Ayame.
     The  easy  way:  At the level select screen, hold Square + Circle
and press R1, R2, L2, L1, Up, Down, Left, Right, Select.

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Mission Editor codes:

More options:
     The  farther  you  reach in the game, the more options you get in
the  mission  editor.  You  can  use  the same tilesets in the mission
editor from the current mission you are playing.

Unlock All missions:
     At  the  Custom  Mission screen, hold R2 and Circle and press Up,
Down, Down, Right, Left, Left.

Copy Missions from CD (U.S. Version):
     At the Mission Settings menu, hold Circle and press Up, Up, Down,
Down, Left, Right.

Copy Missions from CD (PAL version):
     At the Mission Settings menu, hold Square and press Up, Up, Down,
Down, Left, Right.

Office tileset:
     At  Edit  Mission  screen,  choose New Mission, hold L2 and press
Circle,  Square,  Left,  Right,  Circle,  Square.  Tenchu, Inc. custom
mission: Highlight Create New Mission. Hold R2 and press Left, Square,
Left, Square, Right, Right, Circle. Press X.

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PAL verison codes: 

Level select:
     At  the  level  selection screen, highlight a blank mission, hold
Square  and  press  Right, Left, Down. Release Square and hold Circle.
Then,  press  Left,  Right,  Up.  Dont  release Circle, press and hold
Square as well and press Up, Down.

Direct kills [story mode]:
     Pause  and  press  R1,  L1, R1, L2. Then, hold Triangle and press
Down, Down, Down, Up. The game will restart.

Unlock All Ninja Items:
     At  the  item  selection screen, press R2, L2, R2, L2. Then, hold
Select and press Right, Left, Circle, Square, Down, Up, Up.

Increase Item Inventory by 1:
     At  the  item selection screen, hold R1 + Circle and press Right,
Down, Left, L1.

Show Entire Map:
     During the game, hold select to view the map and hold Select + R1
and press Circle, Circle, Circle, Circle, Circle.

Regain health:
     Pause the game, hold Circle and press Left, Right, Up, Down

Play as Tatsumaru:
     The hard way: Beat the game with both Rikimaru and Ayame.
     The  easy  way:  Highlight  a character, hold Circle + Square and
press  Right,  Up,  Left. Dont release Circle + Square, press and hold
Down  as  well and press L1, L2. Keep holding Circle + Square, release
Down, then press Select.