I often crack my fingers because of cramps & pains due to various activities - writing/typing a lot, other sorts of handiwork etc. Of course we're not talking about terrible pains, but there is a physical discomfort, not a psychological reason.
I crack my toes after walking long distances and/or wearing tight-fitting shoes that get them in cramped positions.
90% of my attempted back/spine cracks are purely in order to relieve back aches and pains. My back cracks are tiny, barely audible if you're not standing right next to me, but the relief from physical strain & pain is tremendous.
Occasionally, even a good neck crack might help in the case of a headache/migraine. I don't try to crack my neck often so… don't quote me on that... but, you get the picture...