Are you marking for hand quilting or hand piecing? If you're marking sewing lines for hand piecing, then just about anything that doesn't bleed will work, because once you've sewn the seam, the lines are on the back. I've used pigma pens to mark my hand piecing lines.
For hand quilting, you'll have to test different markers to make sure they come out of your fabric. My favorites are Prismacolor colored pencils in light blue and white, a Bohin ceramic lead marker in white, and Clover's white fine line marker. So long as I make light marks I've had no trouble getting these out, but like I said, the key is to test them first.
Janet