In the past I've used a special CD-R marker to write on CD-R's. But I'm wondering if it's OK to just use a regular felt-tip marker (Sharpie, etc.). (Obviously, a pen that you have to use pressure with (ballpoint, etc.) would NOT be safe.)
The danger is that there could be a chemical reaction between the components of the marker's ink and disk's surface. Some "permanent" markers are quite aggressive, and while the damage is not immediate, it could happen over time. Council on Library and Information Resources says in their report:
Numerous CD vendors have noted that the thin protective lacquer coating can deteriorate from contact with certain solvents in markers. To eliminate the risk, water-based markers are recommended for CD labeling. As a solvent, alcohol is generally less damaging than xylene and toluene, which are common in aromatic solvent-based markers. According to anecdotal reports, alcohol-based markers can be used to label CDs without causing performance problems. However, there are no explicit lab test results to show what effect solvents in markers have on different CDs or DVDs, particularly over the long term.
Regarding Sharpie markers specifically, this is what Sharpie's FAQ says:
Newell Rubbermaid has used Sharpie markers on CDs for years and we have never experienced a problem. We do not believe that the Sharpie ink can affect these CDs, however we have not performed any long-term laboratory testing to verify this. We have spoken to many major CD manufacturers about this issue. They use the Sharpie markers on CDs internally as well, and do not believe that the Sharpie ink will cause any harm to their products.
Add my 2 cents here. I have been using Sharpie brand markers to label discs for years. Never saw any effect either short term or years after. I have even used isopropyl alcohol to "erase" the markings. However, I do generally write fairly lightly so as not to scratch the surface and force the solvent deeply into the top coat.
Having said that, different brands make discs of differing amounts and types of materials. Basically, you have polycarbonate plastic disc as the carrier to which a layer of aluminized film is laminated. The information is written to the polycarbonate disc side of that film. That's the important part to not damage. To protect that, it is then over-coated with a layer or 2 of lacquer with the logo and what not and the top coat to seal all that.
Any reaction from using a Sharpie will likely be in a matter of seconds. The dangerous part is the solvent used. Which does eat somewhat into the lacquer to bond the writing to it. But probably not enough to eat completely though that to the film below. However, that would depend on the lacquer formulation and it's base which is used and how thick it is applied.
Once the solvent evaporates, I doubt there is any further chemical reactions occurring. If so I would be looking for a different brand of discs, because many other things in the environment would be also reacting.
Even if you eat through the lacquer, you'd have to also eat into the film carrying the information. At least enough to distort the film from being flat.
However, there are pens made specifically for disc labeling if you really want to be careful. And if your data is that important I'd be making 2 or 3 or 10 copies using different media brands and types. Then store and mark them differently and separately. Discs are cheap. Data is not.
Might also add here that there is a difference between writing a label and sketching a label. Writing applies very little solvent. Sketching will apply more solvent in a concentrated area and have more of a damaging effect.
There is lots of experience (mine included) to support the use of Sharpies (brand) markers on CD-R and DVD-R. There is less experience with the longevity of Sharpie-marked CD-R and unmarked CD-R. If you're going for archival storage you will probably do best (in general) if you use considerable care in handling of whatever media you use, and CD-R may not be the best choice in the first place.
That said, I mark my optical media with Sharpies.