I was using the little round dot stickers in different colors that I got from work but after awhile they paper starts to fray and wear off and just looks crappy. I been meaning to look around for some vinyl or plastic dots that will last. Ive also found that electrical tape and a permanent marker works and holds up pretty well.
ETA
Just found these, I think they will work well. Since their transparent there obviously not paper so they should hold up. These are nice b/c their different colors plus you can label them. They also stay stuck on but you can easily pull em off without leaving a bunch of sticky crap!