Get six powerups so that the question mark box is selected. Then, when the thousands digit of your score is a five, get a seventh powerup and you will get 10,000 bonus points.
30 lives, player one
At the title screen, press Up, Up, Down, Down, Left, Right, Left, Right, B, A, Start.
30 lives, player two
At the title screen, press Up, Up, Down, Down, Left, Right, Left, Right, B, A, Select, Start.
Continue playing
Quickly press Down, Up, B, A, B, A, B, A, B, A after you've lost your last ship.
Full power-up
While playing, pause then press Up, Up, Down, Down, Left, Right, Left, Right, B, A, Start.
Warp to level 3 after defeating Core Fighter
In level 1, when the thousands digit of your score is even, destroy 4 hatches.
Warp to level 4
Destroy Xaerous Core at end of level 2 within 2 seconds of its core turning blue.
10,000 Bonus Points...