I’m taking a few extra rest days this week — I seem to be more sore than usual and it’s causing me to start regretting getting up every morning. My head is not in the game.  I am forcing myself to let my body heal by resting and doing some extra mobility work. I have been reading about DOMS and how to handle it — In the CrossFit journal:

Muscle Damage and Soreness: An Overview
You probably don’t need me to explain that the major reason why DOMS is a recurring theme in CrossFit is the emphasis on constantly varied movement patterns. A specialized athlete will typically use similar muscle groups day in and day out. Thus, the specific muscles concerned will adapt and become quite resistant to muscle damage and DOMS. The CrossFit athlete is using a far greater diversity of muscle groups with constantly differing movement patterns. The result is that we will regularly be hitting muscles with unaccustomed exercises. Voila! DOMS is inevitable in this scenario. 
Should you train if your muscles are sore? There are many fitness experts who would tell you a flat “no.” Well, the real answer is: it depends. You are the owner of your body and you need to make that call for yourself. Mild to moderate DOMS is unlikely to be a problem. However, if you have severe soreness in a particular muscle group I would suggest that you provide that body part with some relative rest. An example: if you have severe soreness in your legs from squatting during Cindy, then you would be prudent to avoid attacking a workout with heavy back squats the next day (a very similar movement pattern). I see less of a problem if you run on those sore legs, as the movement is quite different from what caused the damage. Just be aware that your run performance will probably suffer in comparison to running on fresh legs.
Note that chronic muscle soreness that seems to linger for longer than usual may be a sign of over-training, or der-recovery, whichever way you choose to look at it. If you are feeling unusually unenthusiastic about your training, and you are noticing chronic muscle soreness, you would be well advised to listen to your body and take appropriate rest until your body and mind are back in the game.