Researchers finally solved the mystery.
Using a virtual knuckle, researchers simulated the process known as tribonucleation, the making and breaking of contact between solid surfaces immersed in liquid. The bones in the knuckle joint touch and separate all the time, leading to reduced pressure in the synovial fluid trapped in the spaces, which in turn forms bubbles.
http://amp.timeinc.net/time/5220275/knuckles-crack-science-why-reason