I just stumbled upon a post from IMA_FARANG at thaivisa.com which is a good match to the initial post in this thread:
I have been told by many busy-body types that my habit of clicking my joints (fingers, toes, etc) will cause me problems later "when I get older" since I was 12 years old. I am now almost 60, and I haven't seen the effects yet. For that reason I have to vote with the "no bad effects" side.
My understanding is that the click is simply a release of gas around the joints, and totally harmless. However, I expect their will be some expert on here who will tell me differently.