Delayed Onset Muscle Soreness

Noakes has a good section on this topic (Noakes, 1991, p524-526).  The DOMS is very often associated with eccentric contraction (e.g. downhill running).  It is due to damage to the connective tissue in the muscle.  The characteristic feature is that pain develops when the muscle is forcefully stretched.  One hypothesis is that the damaged muscle cells die due to calcium inflow; then initial inflammation stimulates nerve endings causing pain.  The damage site is Z-band and is more pronounced in Type II muscle fibers.  Another hypothesis is the the exercise-generated free radicals attack cell membranes leading to their death.

The most important measure to cure DOMS is resting the damaged muscle.  The following steps should be taken:

1. Ice the sore muscle to reduce the initial inflammation and rest the concerned muscle.  Exercising other muscles is OK.  This should last for two or three days.
2. Stretching is OK, but must be very gentle on the sore muscles. Stretching should stop at even the slightest pain of the injured muscle.
3. When the pain fades significantly (usually in two or three days),  use deep tissue massage to help break the scars and eliminate any knots. 
4. After the pain fades, resume the exercise on the sore muscle very cautiously.  Increase the intensity very gradually.  Listen to the body very carefully and stop or reduce the intensity of the exercise immediately if the pain recurs. 

DOMS prevention:

1. Since DOMS is one of the symptoms of overtraining, don't overtrain.
2. Increase the intensity of workouts with high eccentric muscle contraction (e.g. downhill running, speed work) very gradually.
3. Distance training and weight training.

Reference:

Noakes, T (1991) Lore of Running. Leisure Press, Champaign, Illinois.