Most of us learned to stretch in middle school gym class. For example, to stretch the hamstrings, we learned to stand with one foot crossed over the other and then bent over to touch our toes (or made a brave attempt). Problem is, we all learned it wrong.
How can that be? Well, consider your gym teacher. Where did she or he learn it? Probably not a physical therapist, kinesiologist or exercise physiologist. It's just the way she or he was taught, probably in junior high. There's no real science or reasoning behind it. Yet most people (even trainers and coaches) persist in teaching us to stretch that way. I've learned a lot about stretching from a book called The Stark Reality of Stretching, by Dr. Steven Stark. You can buy this book for 3 cents on Amazon--not joking. Or, give me a heads up and I'll have it in my office for you to borrow.
What this book explains is that certain muscles in our bodies are stabilizers; meaning, they stabilize our joints so that we can safely execute movements without falling over or hurting ourselves. Stabilizer muscles are almost always partially contracted--they have tonicity--because that's their job. They are controlled unconsciously by our brains, and it's very difficult to turn them "off" consciously. Our hamstrings are an example of stabilizer muscles. Yes, they powerfully flex the knee; but more importantly, they stabilize the pelvis when we are standing.
What does this mean? When you are standing, and bending over to stretch the hamstrings, the said muscles are firing like crazy to control your pelvis. In other words, they are NOT STRETCHING. Quite the opposite: they are shortening so that you don't pitch face-forward onto the ground. That "stretching" feeling you experience in the backs of your thighs during this maneuver is likely the sensation of tearing muscle fibers that are loaded beyond their capacity. You could also be stretching your glutes, paraspinals (in your back), or calves. But you aren't stretching the hamstrings.
So how should you stretch? Take gravity out of the equation: if you are in a sitting position with your weight resting on your sit bones, then your hamstrings have no work to do and they can relax. Alternatively, you can lie down on your back (my favorite) with your leg resting up against a wall. A doorframe works well for this because there's someplace for your other leg to go.
Either way, aim for a gentle stretching sensation. Your body is smart: it has stretch receptors strategically placed in the belly of every muscle. These stretch receptors detect changes in length of the muscle, and most often the body's response to a lengthening muscle is to contract, or shorten, it. The more aggressively you challenge the the muscle by forcing it to lengthen, the stronger the contraction response. Therefore, aim to fly under the radar by stretching very slowly and very gently. You should feel distinctly under-challenged, but that's ok. Again, you should only feel a very mild stretch.
There's tons more about how to stretch effectively and how to stretch different parts of the body, so I encourage you to either get the book, or talk to me. Your body will thank you.