Head over to the whiskeypail-test blog and read through the workflow post (and his other posts as well). I'm all for a structured workflow and his approach sounds good.
Of course each shot will ask for workflow adjustments, but through my years of finishing shots or picking up shots by other people I definitely appreciate a "clean" scene. When you're done with your shot and you got a second, make sure to clean up your shot file in case someone else has to pick up your shot at a later date for whatever reason. You will make many people happy. :)
