I get this too! The problem is that I tend to get the urge to click my shoulders back to relieve tightness/aches, that then causes it to crunch and crack and then in turn results....... pain.
All I can think is that it involves tight tendons/ligaments that need releasing.

I very recently had first rib excision surgery and while in hospital I forgot myself and over stretched to reach something which resulted in an almighty crack!!!!!!! It sounded like a bone had broken...... then it dawned on me that the bone had been removed in that position. I called the nurse who said that it was most probably a tendon that had crossed over something during surgery that was pinging back into its position????? Anyway, initially it hurt but very quickly settled so I guess she was right?