A frequent complaint from people is that their joints 'click', 'crack' or 'pop'. The qusestion is whether this is normal or something to worry about, and of course why does it happen. So in quick order yes it seems that it is normal, no don't worry unless the 'click', 'pop', 'grating' is painful. Ask for advice/help maybe from your friendly local osteopath. Pain is your body's alarm system, it's sent to you when your brain considers that you need to reconsider what you are doing. Don't ignore it.
As to what causes the painfree noise..thats a QI 'nobody knows' answer. There are some thoughts that gas can expand into a vacuum caused by joint movement. Sometimes it's not joints but muscles or ligaments/tendons moving over each other. Either way apart from being slightly annoying to some people it's a normal natural human sound. Of course what isn't normal or natural, is when somebody constantly cracks their knuckles or neck. Whilst it's probably untrue that the constant cracking will cause arthritis, it is probably true to say that it's a most irritating habit. (and yet somehow compulsive)