First, move the cursor in a shop above or below the item you wish to buy - whichever item you hover over preferably should have a cheaper cost than the item desired. Then press Up or Down on the D-Pad (towards the desired item) and the A Button at exactly the same time - you should buy the item you wanted, at the cost of the item you hovered over!
Press and hold A and B on Controller 1, then turn the console off and on again. After, during gameplay, access the status screen via Start and press A on Controller 2. This enables very quick movement. Press any D-Pad button for invulnerability, all items, all equipment, and max (255) MP as well.
First, you must equip a sword that can charge to the second level, as well as the ball to go along with it. Hit Select and bring up the menu again, then swap to a sword that cannot charge to the second level. Keep the menu up and save the game, then reset - the newly-equipped sword will then be able to charge to the second level!
To pause the game, press B on the second controller.
If you use the Rabbit Boots, normally you can jump, but there's a special glitch involving the dolphin and these boots. If you were to get on and get off the dolphin while jumping with these equipped, you could hit the water, and in turn fly over the water. This glitch can be used, for example, to skip the Evil Spirit Island sequence.