The thing about the CD players being banned but CD-ROM drives in laptops being allowed is a matter of headphone leads. You'll also find a ban on external mice on laptops, for the same reason.
What happens inside a CD player/ROM drive is that lots of energy is used at radio frequencies -- not normally directly on the aviation or nav bands, but with significant amounts of spillover there nonetheless. A digital signal at 1MHz will also have stuff going on at 2MHz, 3MHz... all the multiples of the basic frequency, in fact. Normally, this is shielded by the case and doesn't escape -- this is a condition of modern electronic equipment passing various interference regulations.
If you plug a lead in, though, it acts as an antenna and can couple the signals inside the case to the outside world. Headphone and mouse leads do this -- in theory, this shouldn't happen and there should be components in the CD that block the signals before the headphone/mouse socket, but in practice it's not so clear cut.
The more I think about it, the more it seems that making some form of hand-held/seatback sensor for emission detection would be very useful. If I could make one for £500 or so, would any airline buy it?
R