Extra Ending Scenes
There is an extra scene that you can see in the ending, simply by waiting for about two minutes after the words 'THE END' appear on screen.
Hidden Boss
While traveling through the space station Omnitopia, you will eventually come across a console into which you must input a code to continue. Try all 27 possible codes (variations of the order of the numbers 1, 2, and 3) until a door opens above. After entering the door, you will face an interesting boss.
Infinite call beads
When you reach Nobilia, go to the front gate where the two guards are at. When you are in front of the two guards, go down to the first right corner of the fountain where a call bead can be picked up. But keep pressing the action button really quick until you load up on 99 call beads.
Infinite run stamina
With any weapon that has reached level three you can exploit an infinite run glitch. Hold down the attack button until the weapon reaches its maxinum charge level, continue to hold the attack button, while also holding the run button.
Profanity punishment
At the start of the game when you enter your name, enter one that contains the 4-letter F word. When you reach the skeleton in the desert, he has new dialog calling you a potty mouth, and he charges you 3 Amulets of Annihilation to board the ship instead of the usual single amulet.