the best permenent pens to use on fabric are micron pigma pens- they are acid free- archival quality permenent fabric markers with fine tips- they do not bleed or fade.
i usually design my labels on the computer and then print them onto fabric prepared for dyeing.
on my label i include the name of the quilt, my name, state, date, care instructions, fiber content, and if it is a personal (for someone specific) quilt i include information about the occassion or person.
some people embroider labels too.