Purely to stop my procrastination before heading out the door for a run, I decided to stretch before I went downstairs to put on my running shoes.
What I found is that when I stretch barefoot, the stretches are actually a lot more effective and can be done more accurately. I don't know if having running shoes on just tends to move your foot around or if they restrict your movement a little. I'm not sure what it is, but I know that I get a much better stretch when I do it barefoot.
I find that especially true in calf stretches (on carpet) where you're leaning against a wall. I find that when I stretch the non-extended leg that I can still keep a stretch on the extended leg. (See the picture at left, obviously not me.)
Since I've been doing it, I've noticed less tightness when I'm running and afterward. Nothing like getting back to basics, eh?