The Legend of Zelda: The Wind Waker Cheats

In the battle against puppet Ganon's human-like form ( Note: Puppet Ganon) hookshot up to one of the platforms. If puppet Ganon punches you, you should go through the wall. You can still hit puppet Ganon with Light Arrows, but he and the keese won't be able to hit you.

When fighting Gohdan, stay in the doorway and his hands can't touch you. This is the easiest way to destroy them.