Now researchers may finally know why. Apparently the noise is caused by microscopic bubbles when they pop. Summer Delany, PIX11, explains:
Your knuckles are surrounded by fluid, and when you stretch and move your joints, the pressure creates bubbles. When those bubbles collapse, a sound is produced.
And no, cracking your knuckles doesn’t cause arthritis, but “[c]hronic knuckle-crackers [are] more likely to have swollen hands and reduced grip strength.”