Sometimes joints "pop" on their own and sometimes they are manipulated in a way to force them to "pop". It really is not the bones that are popping. There could be a couple of reasons why joints make this popping noise. Chiropractors often explain it as gases escaping the joints. For example, when a chiropractor performs an adjustment on someones neck it often makes that popping sound. This is the usually the sound of gases being released, not the bones being cracked. Synovial membranes inside a joint contain fluids. In these fluids there is carbon dioxide, oxygen, and nitrogen. When the joints are manipulated in a certain way, these gases can be released, causing the popping noise.
When you "pop" your joints you are temporarily displacing them out of their normal position. The pressure in synovial fluid (essentially a lubricant) in between the bones is reduced when you do this. As a result bubbles form, expand, and then burst creating the popping sound that you hear. It is a process called cavitation - air bubbles forming in a fluid. The reason you can't pop your joints for a while after this is the gas you've released the first time needs to be dissolved back into the synovial fluid. Once this happens you can crack them again. Contrary to popular belief, no serious long term damage has been found in any research on chronic joint poppers.
Another possible cause of the popping sound is your muscles, like say for instance when you crack your neck. Contrary to popping your joints, doing things like cracking your neck can cause permanent long term damage because you are stretching the ligaments. It's a viscous cycle because cracking your neck loosens the muscles and makes you feel temporarily better, but then they get even tighter to compensate for the loosened ligaments. Repeat cycle.