QUESTION!
Simpsonsfan, are these scratches located near the eject, power and reset buttons? If so, deal with it, the majority of GameCube's have minor scratches, or even hairline cracks around these areas. Very easy to notice on the Jet Black GC. It's to do with how the plastic is set.
Now, if you're talking about scratches on the name plate (the big round thing on top), deal with it. It's a bitch, and scratches with extreme ease. They can however, be replaced for a minimal amount of money. Or if you live in Europe, just subscribe to 'Cube' magazine. They have awesome name plates included with the mag on at special times (I'm guessing they'll include another Zelda one when they review the PAL version)
FINALLY, if these scratches are elsewhere... Boo hoo. Do you have the GC sitting in your lap, laughing at you when you play it? No. Nothing can remain in perfect condition, unless you keep it in the box. And that would be sad.
And yes, towels suck. I used to cover my GC with a tea-towel and found I was getting very small scratches on the name plate. I switched to an old T-Shirt. Ahhh, the too small Garfield shirt I got for Christmas back in 2000, finally getting some use =)