There are many things you can do. If you do use a permanent marker, try to find one that is archival, otherwise labeled as acid free. They are less likely to damage fabric over time.
I have made labels out of muslin or a scrap of light fabric used in the quilt and signed it with an archival pen. I have also hand embroidered labels before. You can find pre-printed labels that you simply personalize with same pen. You can print a label using fabric sheets designed for ink jet printers. You can make labels with an embroidery machine (or have a friend make one). I have also heard of quilters printing info with a pen under the binding, so that the label cannot be removed in case of theft. This way, if the quilt is recovered, it is easily identified. I'm sure that there are loads of other ideas out there...