I use a copic multiliner. A while back I saw a blog post where someone tried out the different types of pens and washed the fabric and the multiliner was one of the best. I bought mine from
http://www.copicmarkers.com
I ironed the label to freezer paper and then wrote, and then removed the paper and sewed it on by hand.
I've only labeled one quilt though-I made it for my MIL and I'm pretty sure she'll never (or rarely) wash it or use it. You never know though. She has it on the back of her couch.