When you pop a joint, such as a knuckle, that area is subject to rapid movement (as the pressure build up releases and you are still applying excessive force), and ligaments e.t.c. may be stretched beyond their usual range of motion. This is a mild shock to the body, which perceives this movement as unexpected and potentially damaging, which then releases endorphins in order to manage any pain that might arise from potential damage, and try to reduce inflammation. Endorphins make you feel good.
EDIT: For clarity, I’m not saying that the ligaments overstretching is responsible for the pop in any way, I am saying that the sensation caused by a pop or a crack is enough to convince the body to release endorphins in that area, regardless of whether there is any pain/damage or not. It is the endorphins that we perceive as pleasure.
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