Level select:
Press B, Select, Left, Right, Start at the title screen.

Twenty-five submarines:
Hold A + B, then press Select, Up, Down when the sub course is being laid out.

Twenty-five missiles:
Hold A + B, then press Up, Down when the sub course is displayed.

Twenty-five fuel units:
Hold A + B, then press Select, Left, Right when the sub course is displayed.

Twenty-five silent runnings:
Hold A + B, then press Left, Right at the mission selection screen.