Level Select
At the main screen (where you choose One Player or Two) press B, SELECT, LEFT, RIGHT then press START.
Extra Silent Runnings
For 25 Silent Runnings hold A+B then press LEFT, RIGHT on the mission screen.
Extra Ships
For 25 submarines, hold A + B, then press Select, Up, Down 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 Fuel
For 25 fuel units, hold A + B, then press Select, Left, Right when the sub course is displayed.