Chip's CD Media Resource Center:
Article: Labeling -- Will A Sharpie Ruin My CD-R?

Labeling -- Will A Sharpie Ruin My CD-R?

As a longtime fan of the Sanford Sharpie marking pen, this was a big question for me. Fortunately, it was answered very directly by Robert Starrett in an article CD Printing, from Sharpie to High-End Color appearing on the Roxio web site.

In short: go for it, use your Sharpie all you want. There appear to have been no reports of the Sharpie ink affecting the recording. And since it's a soft tip pen, you won't physically damage the metal layer.