Depends on what and where I'm marking. Since I hand piece and quilt everything, I mark the seam allowances on all of my pieces, as well as cutting lines and to do that on the lighter stuff I use micron archival markers.
I will sometimes use a regular #2 pencil with a VERY sharp point, and at times the silver or white pencils designed for quilting.. I don't trust the "disappearing" ink pens as after they had been out a short time, they were found to deteriorate the fabric. Just left me uncomfortable, so I didn't use them.