Stretching is not a legitimate means of cooling down. It is only part of the process. After you have completed your workout, the best way to reduce muscle fatigue and soreness (caused by the production of lactic acid from your maximal or near-maximal muscle exertion) is to perform a light warm-down. This warm-down is similar to the second half of your warm-up (but in the reverse order). The warm-down consists of the following phases:
1. sport-specific activity
2. dynamic stretching
3. static stretching
Ideally, you should start your warm-down with about 10-20 minutes of sport-specific activity (perhaps only a little more intense than in your warm-up). In reality however, you may not always have 10-20 minutes to spare at the end of your workout. You should, however, attempt to perform at least 5 minutes of sport-specific activity in this case. The sport-specific activity should immediately be followed by stretching: First perform some light dynamic stretches until your heart rate slows down to its normal rate, then perform some static stretches. Sport-specific activity, followed by stretching, can reduce cramping, tightening, and soreness in fatigued muscles and will make you feel better.
According to HFLTA, "light warm-down exercise immediately following maximal exertion is a better way of clearing lactic acid from the blood than complete rest." Furthermore, if you are still sore the next day, a light warm-up or warm-down is a good way to reduce lingering muscle tightness and soreness even when not performed immediately after a workout. See section Pain and Discomfort.