Thanks ZigZagMan for bringing this up!
Besides using wax, there are specific chemical solutions for removing scratches, like solutions that remove scratches from plastic eyeglasses.
A quick search on google yielded this: (Looks like such solutions have been available for years...)
Go here to see a collection of reviews about one such product:
Here is an excerpt from one of the reviews which explains how it works. Yes, they also say that wax or fillers can flake and damage the drive!!!
Wipe Out! CD Repair Kit
By Logan Harbaugh (What's Hot Editor, InformationWeek Magazine)
September 29, 1997 Issue 650
"...Yes, there have been many other products claiming to cure compact disc damage but Wipe Out! is unique in that it isn't a wax or filler. Those types of products can cause damage to your CD player or CD-ROM drive by flaking off inside the drive mechanism. Wipe Out, on the other hand, is a polishing compound specifically designed to interact with the plastic coating of a compact disc. Instead of just filling the scratches, Wipe Out actually allows you to buff them out permanently. To work its magic, Wipe Out combines three active ingredients including... "a chemical which evaporates quickly and prepares the surface of the CD by "melting" a micro layer of the CD plastic coating, a microabrasive compound which polishes the disc with your help, and a hard wax in liquid form which suspends all of the chemicals long enough to produce the desired results."..."
Copyright (c) 1997 CMP Media Inc.