Extra Fuel  -  For 25 fuel units, hold A + B, then press Select, Left, Right when the sub course is displayed.

Extra Missiles  -  For 25 extra missiles, hold A + B, then press Up, Down when the sub course is displayed.
Extra Ships

For 25 submarines, hold A + B, then press Select, Up, Down when the sub course is displayed.

Extra Silent Runnings  -  For 25 Silent Runnings hold A+B then press LEFT, RIGHT on the mission screen.

Level Select  -  At the main screen (where you choose One Player or Two) press B, SELECT, LEFT, RIGHT then press START.

Gameshark codes

Infinite Lives
010332dc

Infinite Energy
016333dc 

Infinite Shield
010331dc 

Infinite Torpedos
010330dc