Ganondorf
To beat Ganondorf's Puppet form, you have to hit each of the Strings that are holding him up twice with the Boomerang. Once he falls down - get behind him and shoot that Blue Orb on his Tail with a Light Arrow...repeat two more times.
To defeat his Spider Form, use the reflection on the water to see Ganondorf spinning around on the ceiling. When he stops spinning, he will come down - so run to the side where the Blue Orb will be and when he hits the ground, shoot a Light Arrow at him...repeat two more times.
To destroy his Snake Form, you'll need some luck - stay out of his way and shoot Light Arrows at the Blue Orb. Plan ahead when shooting, you could also try hitting his head to stop him...but three hits will take him out.
Wait - you're not done yet, don't get too excited...
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