Did you know that it is the top (labelled) side of a CD is the side that needs most care? The underside of the disk is just a plastic protective layer. It is the upper side is where the laser written data exists. The upper side has a much thinner protective coating.

So if you label a CD never try to peel it off again. It could peel off more than you bargained for. If you write directly onto CDs make sure you use a pen made for the job otherwise the ink could react with the upper layer and damage the important ones below. If you leave CDs kicking around outside of their cases always best to rest them shiny side down. That isn’t to say you can scratch the shiny side that much but minor scratches shouldn’t hurt.

I am looking at a data CD and am getting really confused - the information is on the top?

Yes it's true but perhaps best explained in this link, I think click here but here's a condensed version. From the top down the CD consists of a thin protective layer, a metal reflective layer (silver or gold), a photo sensitive dye layer and plastic protective layer. The laser fires its beam at the dye layer and burns a hole in it which then fills in with the metal layer above. This is all very microscopic and happens lots of times when a CD is being written.

Anyway, the link above gives a more comprehensive explanation about a CDs construction and how to look after it.

So I shouldn't write with a black sharpie onto the CDs I've burned?

When I was browsing around on Google for info. on marker pens I came across a forum debating such things. A few people said they'd been using sharpie pens for ages and hadn't had any trouble.

But I suppose you might as well use proper CD-R marker pens just in case. I just bought a pack of 4 various coloured ones. Not too expensive and very decorative!

No, You shouldn't. Markers are best for such purposes.
Actually one shouldn't stick one of those stickers too (ideally)
because the damage is done if the top coating is gone
I learned it the hard way!

A black sharpie is a marker - one of the ones with the felt tip...

Well, I guessed you meant ball point and you can colour the other side with a marker pen if you have problems with certain cds.
Ask Sony - they learned it the hard way

If you write on the clear plastic non-data bit in the middle it wouldn't matter what pen you use. I suppose you'd have to have neat handwriting though.

So that rules me out of doing it!