That depends. I hold the stretch with the emphasis on my proper posture (straight back, for example, in the seated leg stretch). I observe to see if I am adhering to the principles of stretching as outlined by my Teacher to me. I wait until the muscle releases in that position then go down further. This may take a few seconds for stretches that I am proficient in, or several minutes if I have had an injury or if it is a muscle group I have neglected.
Lets take a practical example. Check out page 2 on howtstretch.com, which shows groin stretches
There are three areas that are being stretched here. Inner groin, outer (lateral)thigh, and back. I find that when I first get into the position, one of the three (let's say back) is tightest. When that releases, which may take a minute, I come forward, and feel the inner groin. When that releases, I feel my outer thigh. There is no rule as to which I feel first, it can be any of them. Each may take a different amount of time to release. Then when all three have released, I usually hold it for another few minutes.
Another training technique I use is different times for different body sides. Example: my right hamstring was always looser than my left. I got into the habit of holding the left side for a longer time than the right side to correct the imbalance. So, if I stretched over the right leg for two minutes, I stretched over the left for three. You will be amazed at how you can correct imbalances this way. Give it a try!