This is definitely a recent thing, but I have not done anything that would have injured my neck.
Have you fallen and banged your head, or have had any injury to your neck or shoulder areas? Your neck muscles could be stressed or very tight, not allowing you full range of motion at times. Exercises, yoga or massage therapy could be non-invasive way to start. These have all helped my "clicking neck" to some degree. If it becomes really bothersome or painful you should go to your health care provider who can give you advice.
Just like popping your knuckles. Gas builds up between the joints and when we release it, it pops. Perhaps the escaping gas from your neck just doesn't have enough pressure to "pop" and make a sound.