Ah, the joy of resuming a training regime. The feeling of accomplishment, basking in the sweaty glow of hard work. The adrenaline rush after finishing a heavy set of squats. The heart pounding of doing a WOD for time, and actually pushing yourself.
Waking up the next morning to screaming muscles, unable to fly quickly down the stairs. The inability to sneeze without searing pain in your abdomeninal musculature. Lifting your arms to blow dry your hair, only to find that they don't seem to reach as far as they used to.
DOMS. Delayed Onset Muscle Soreness. The muscle pain and soreness that occurs roughly 24-48 hours after exercise. Most often at the beginning a new exercise program, a change in your sport, or a significant increase in exercise intensity. In my case, it's the welcome back present after a month away from the barbell.
Luckily, the pain is fleeting. It lasts just a few days, and rarely reoccurs. More importantly, it's a normal bodily response to unusual (or somewhat forgotten) exertion, and is part of the pysiological adaptation process that will eventually lead to increased strenth and endurance as the muscles rebuild (think "Better, stronger, faster" like the Six Million Dollar Man).
According to a Google search, the #1 treatment for DOMS is to wait. Just be patient and it will subside on it's own. You can sit in an ice bath, take a non-steroidal anti-inflammatory (though I'd be careful with those), do Yoga or get a massage. Personally I subscribe to more of an active-recovery technique (a.k.a, suck it up and keep on going). Obviously you should avoid anything vigorous that aggravates the existing discomfort (here's a perfect example of "Do as I say, not as I do").
I was surprised to find that there is no evidence that stretching is helpful, nor is performing a cool down after exercise. However, warming up (particularly before a new and unfamiliar movement) results in a small reduction of the onset of DOMS symptoms.
I should point out, as well, that there is a different between the pain associated with DOMS is different than the acute pain resulting from an injury - if the pain is sudden, specific and accompanied by bruising or swelling (or blood), stop and take stock and treat the injury as advised by a doctor or sports coach.
Hobble on, oh brave weight room warriors. Hobble on.