New Scientist explains the wince-inducing experiment that produced the video:
Gregory Kawchuk at the University of Alberta, Canada, and colleagues used a cable to slowly pull a man’s fingers in an MRI scanner until the joints cracked. The sound was thought to come from the collapse of an air bubble, but in the scans the air cavity that formed in the fluid around the separating joints persisted after the noise.
So the mystery remains unsolved, but the good news is that, contra the myths surrounding the practice, scientists think that it’s harmless. So crack away, everyone.