So I accidentally took a Good Housekeeping magazine from the doctor's office waiting room. (current issue - November 2011) On it's Ask Heloise page, one of the questions is about removing dog scratches from a wooden floor. The answer reads: "Take a pecan or walnut, break the meat in half, and rub it into the scratch. Go with the grain of the wood (you'll feel the nut meat getting warm) to fill the scratch. Buff with a soft cloth."
There is more about using crayons and such, but that's the relevant part for here. Yes, seriously. Fill scratches in your hardwood floor with nut meat.