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Glitches brought to you by 
Music from one place to another
Before entering a pipe, enter it with Mini-Mario. During the Pipe-Selection Screen, the music in the previous area you were just in will stay the same. When you warp to your destination, the music in the pipe will now be the BGM until you leave the area/go into pipe while not Mini-Mario, etc.
Permanent Red Pepper Effect!
Red Peppers increase your power for a few turns. During the effect, let the effected brother get knocked out. Then, use a 1-UP Mushroom to revive them. The effect will continue for the whole battle and not wear off! This is especially useful against hard bosses.
Unmovable Mario
Turn Luigi into a surfboard and surf to the coast on the east side of Beanbean Castle Town.
Surf in and land on the shore.
While Mario is dismounting the surfboard, hit a Bob-omb to start a battle.
When the battle is over, Mario will be frozen in the air, but the pause screen will still be accessible.