Knuckles, all the time. I have an unconscious habit of popping them one by one by pressing down on the first joint of each finger with my thumb (of the same hand), and then my thumb by making a fist with my thumb on the inside, not the outside.
I really can't help it. My joints get really stiff for some reason, and aren't 100% mobile until I loosen them up. The popping noise just happens to come with that.
On that note, my left wrist and right ankle make noises every time I move them a certain way.