I used a regular sharpie permanent marker on one of my early quilt labels and it bled out as a wrote, making the wording look "fuzzy". Also over time and with washings it faded a lot. I have had much better results with Pigma pens.
I have also done hand embroidered labels. My current favorite though is stamped labels. I use VersaCraft ink (which is permanent and archival). It is the only ink that I know of which can be used on fabric, but there might be others.