Sometimes I'll be walking and my right ankle starts to click. It *feels* like a ball/socket joint thats popping out and dropping back in but it doesn't hurt one bit. Its done that for years now (I'm 21).
My shoulder does this thing... if I put my right hand behind my head and flap my "wing" like a chicken, forward and back not up and down, it creates a LOUD thumping noise as the bone/joint shifts around. Theres is a noticeable... motion, like when you are pushing a wooden block against a table and you hit a bump and the block stops and then you push a little harder and it suddenly shoots up and over the bump.
My left shoulder can do that too on rare occasions. I can make my right shoulder do it at will but only accidentally on the left.
None of these have ever caused any pain (except the very first time my ankle popped about 6 years ago).
I wouldn't worry about it too much...