Stretching is perhaps the most important component in preventing muscle injury, but people (myself included) often don't spend enough time on it. Our muscles are a collection of elastic fibers. They, along with the tendons that attach them to bones, expand and contract to execute movement. Our muscles are capable of quite a bit of punishment, but proper stretching will maximize muscle performance and maintenance.

The question is often asked, "Should you stretch before or after exercise?" The answer is: Both. Stretching before exercise loosens up your muscles and prepares them for the work you're going to be asking of them. It's often a good idea to do a mild warm-up exercise before stretching, especially if it's cold. Muscles tighten up in order to hold heat in the body. An easy warm-up will get your blood pumping to spread heat throughout your body and start loosening those muscles.

Stretch after you exercise for peak muscle fitness later. As your heart-rate slows, your muscles will start to tighten up again. Tight, inactive muscles are more likely to be sore the next day or sustain an injury. It's also a good idea to keep stretching throughout your exercise if you take any breaks.

As far as which muscles to stretch, you should stretch any and all that get used. Sometimes we don't even realize all the muscles we're using until we feel the tightness. For running, the most important muscles to stretch are the hamstrings, quadriceps, and calves. Those muscles do most of the work in running, but there are many others that get used. Because I tend to keep my arms high when I run, my trapezius muscles (between the shoulder and neck) get strained. I have to make sure I stretch those. The other muscle I feel strain in is my tibialis anterior, the muscle at the front of the shin which lifts the toe of the foot. It's the burning sensation in this muscle that we call "shin splints." Stretching it helps, but the strain is usually because the muscle hasn't been built up enough to cope with much running. Usually the pain goes away after that muscle has been built up.

Maybe I haven't been much help since I basically said "Stretch everything all the time." Mostly, listen to your body. It will let you know when you're asking too much of it.