I found this from my 29wks email:

Physical changes:

Clicking sound? Occasionally, a pregnant woman will describe a distinctive 'click' or 'pop' coming from inside her uterus, usually when her baby is moving during middle to late pregnancy. This is not very common, and it is hard to know what really causes it. One plausible explanation may be the baby's joints rubbing or 'clicking' as they move, but we cannot be certain. In our experience, women who have noticed this clicking sound have gone on to have normal healthy babies, so we don't think it is anything to be concerned about. Perhaps it will remain one of those strange mysteries of pregnancy?