I avoid marking whenever I can by using either Sulky Solvy or Golden Threads paper and quilting through the design. The times that I do have to mark, my favorite product is Blue Line Eraser. I LOVE this stuff! So far it has come out of every fabric that I've tested.
http://www.bluelineeraser.com/
I do occasionally use Crayola washable markers, but always test it first. I had one that didn't come out, but luckily faded enough it wasn't too noticeable. For dark fabrics, I sometimes use tailor's chalk. I have some Frixion pens, but haven't tried those yet.