Noises in the joints, especially the knees, can be quite disturbing and cause concern. Often, these noises are not indicative of any underlying problem. Knee cracking and popping usually has a 'bark that is worse than its bite.' Such noise often persists for years without any real problem developing. If there is no pain with cracks or pops, you can assume it is being caused by the soft tissue in a joint.
In the knee this may occur if the patella is slightly out of alignment and may rub on the adjacent tissues. Noises that are associated with pain may indicate damage to the articulating surfaces of the joint. Such pops and clicks may be due to tears in the meniscus, but are sometimes just due to an overly large or loose meniscus which may snap over the other structures in the knee as the knee bends and straightens.
The bottom line is this. If you hear pops and clicks with no associated pain in a joint, you may want to begin some conditioning exercises to improve the overall integrety of the joint. If the muscles are strong, they will take the weight off of the joint and relax the pressure on those articulating surfaces. If there is pain along with those joint noises, there may be structural damage building in the joint, and it would be prudent to see a physician for an appropriate diagnosis.