What can cause cracking knuckles and toes over time?

To my knowledge No - cause has yet been established for it. It also does not result in any longterm ill effects. However having said that, if someone has it in joint, which has been ijnured in the past then it would be better to have that checked out by your orthopd with an xrays to see if there is a loose body or some other cause for it. Good Luck.