I do labels various ways. I have signed some, I have embroidered some, I have stamped some. I think it is a good idea to embroider a signature for a special quilt, but I wouldn't bother doing that for most of mine. It takes me too long to embroider.
I have used pigma pens a lot, and the quilt I gave my son when he was 2 (he is now 5) has been washed MANY times, more than most quilts get washed in a lifetime, I think
and it is still legible. One of my first quilts that was labeled with a sharpie, on the other hand, is badly faded after just a few washes. Embroidery doesn't last forever, either. My husband has a quilt his grandmother hand-embroidered for him when he was a child, and some of the stitching has become frayed and washed away over the years, too.