Extra high speed mode
Press Up(2), Down(2), Left, Right, Left, Right, B, A on controller two at the title screen. Asaka will say "Excellent" to confirm correct code entry. "High Speed 3" may now be selected on the option screen.
Boss backgrounds
Press L, R, L, R, L, R, A on controller two at the title screen. Select Vs. battle mode game and choose characters. The Metro Train and Studio 6 Stage will now be available on the stage selection screen.
Level select
Press A, Y, A, Y, X, Y, B, A, R, L at the options screen.
Fight as Bosses
Enable the "Extra high speed mode" code. Then press X, Up, Y, Left, B, Down, A, Right, X, Up on controller two at the title screen. A female voice will confirm correct code entry. Choose Vs. mode and move to the left of Shredder to select Rat King or Karai.
Use final attacks in Story Battle mode
Press Up, Left, Down, Right, X, Y, B, A, X, Y, B, A, X on controller two at the title screen. The lower green bar for special moves will appear, just as in tournament mode.
Ten Turtles
Press B(3), A(3), X(6) on controller two at the title screen. The sound of an explosion will confirm correct code entry.
Configure controller
Press Select at the character selection screen.
Using Wingnut
While you are facing an opponent you cannot defeat, use his dive bomb attack (Jump, Down + A). You should be able to defeat even Karai with this technique if you are fast enough.