I think Tom is right, this sounds like growing pains. I guess it could be muscular aches too, that depends on what exercise you do though and what sports you play. The other thing that is could be is poor circulation. The way to tell if you have this is that you will have cold hands and feet.
If you are really sore then you should go to the docs and get checked out, but the chances are he will say that are growing pains too.
I guess it also be a problem with your back too, thats putting pressure on the nerves that go down your arms and legs. You could try doing some gentle stretches before bedtime and see if that helps.