OK, here's the run-down, IMHO-
best sequence is warm-up, then active flexibility or ROM work, then workout, then static stretch IF neccesary.
If you are super flexible by nature, then it is most important for you to work strength at the ends of your ROM in order to protect your joints and connective tissue.
I think rather than stretching everything, people should ask themselves "Which of my athletic movements is hindered by a lack of flexibility?" Then work to see improvement for a specific goal. Once you have sufficient flexibility for the exercises or sports you perform, you do not need more for the sake of more.
google on "active stretching", "dynamic stretching"