I have the same problem but it's not as bad of a problem as it used to be. I know what you mean though - I would crack my neck several times a day and eventually it would feel like it needed popping again, and it would hurt. Right now I feel like I have to crack the fingers on my left hand, but I'm trying to resist it, haha.
I have heard from many people that it is very bad to crack different joints in your body, and that it increases the risk of getting arthritis. This I am not sure of, however, it does make the joints hurt more often, just like you mentioned. I don't know how to correctly explain this, but in anatomy class last year, I learned that some kind of liquidy substance is secreted in the joints to enable them to move correctly, just like oiling door hinges that make noise. Haha, weird example, but hopefully that explains it. I don't know for sure, but cracking joints may decrease the amount of joint fluid secreted? When I think of the long term damage of cracking joints, I think of the disease where the padding is missing in some parts of your spine. It hurts to move your spine then. Lol.
In order to stop, just try to ignore the fact that you feel like you have to pop your joints. One day a while back, my neck hurt really bad because popping it had caused a piece of cartilage or something to fall out of place (something to that effect, but it wasn't serious.. Just something my mom told me happens to her sometimes), and it felt like I had to pop it.. But I tried not to.. and then I tried to pop it but it couldnt pop, so I just let it be. Try as hard as you can to let it be, even if popping it would make it stop hurting.. Because eventually it will stop hurting.. and popping it will just damage your joints even more.
Good luck! :)