It's much more of a b*tch to do than people think. Like, all Ganondorfs image files are ripped from an emulator, and you have to convert those files into another format (TGA->TPL),then you have to use a Gamecube ISO tool to rip the color file for Ganondorf from the game. Whichever color you choose is the color you have to replace, otherwise you won't be able to replace the colors.
Anyway, you make a TPL for the original rip and one for the altered image, and search for the hex code of the original TPL file inside the Ganondorf color file using a Hex Editor, and replace it with the code for the one you changed.
And all the colors for melee are divided into little pieces. Like Ganon's boots are one image, his emblem is another, chestplate, arms, back, cape, and it goes on. Right now SleepyK and I are working on getting all the images online you'd need, and once we do I'll send you a PM.
http://www.smashboards.com/showthread.php?t=247119
That's the guide for it.
Also, I can't stand Michael Jackson, that's why I kept his gloves red. I've been playing with it for a while and it's so much better than Michael Jackson.