Many people seem to think of muscle soreness as a sign of a good workout, but that is not necessarily true. DOMS (delayed onset muscle soreness, the pain that sets in 24-48 hours after a workout) is thought to be the result of tiny tears in the muscle fibers. An old theory blamed it on a buildup of lactic acid, but that premise has been debunked. DOMS can be caused by any type of movement you are not used to, but eccentric contractions (movements that cause the muscle to contract by lengthening) are the most frequent cause. Running down hills, going down stairs and the lowering portion of weight lifting are all eccentric movements. If you do many negative or very slow movements, you are more likely to be sore. Any extreme change to your workout routine can cause a large amount of soreness. It does not mean you have gotten a great workout.
There is no real treatment for DOMS. Despite conventional wisdom, studies have shown stretching to be ineffective. Active recovery (gentle movement) and ice are more likely to help you feel better. The best thing to do is to prevent it from occurring. You can do this by gradually easing into any new activity or program. Warm up thoroughly before your activity (and not by stretching; see the post from Sept. 15, 2010). Allow adequate time to recover. If you are always sore you are not allowing your muscles to rebuild. Rest is as important as your workout, especially if you have built intensity into your program. However, if you never experience any type of soreness it is possible you need to work a bit harder, or to switch up your program.