I would recommend using a CD specific marker for finer writing. However, while regular permanent markers give broader writing, so far I have not had any issue using most permanent markers.
One thing to beware of is to let the writing dry before placing the disc in the drive. Most permanent markers are instant drying, however I've encountered one case where the ink streaked out on the disc when placed in the drive after writing on the disc.
If you need to remove permanent marker from the disc, such as if you labelled a CD-RW and plan on using the disc for something else, scribble over the writing with a black whiteboard marker and wipe away.