I Sharpie markered (is that a word?) the entire borders of a quilt for that exact reason. It's been washed several times and the thread is still black. I used a fine point marker to help keep from getting so much on the actual fabric. Looking back on it now, I suppose a Pigma pen might have been a better choice but the Sharpie is still doing the job.
I guess if you are crazy, I am too. It's always better to have group support!