I've been curious about this for a while now. I generally play a boomkin so I have forms of dots and the general rule I've been using is to let them run their course so you don't over step one tic to refresh it. That always ends up over-ruling the last tic, which increases your time between damage and lessening your damage done over time.
Now, the question I have is knowing that most DK damage is based upon having your diseases up, is it more beneficial to refresh diseases barring the fact you'll lose a tic or letting them run their course and utilizing the different attacks you're given, or would you want to end up re-applying the diseases as they end.