I've been doing this for quite some time, and now my knuckles do hurt from time to time (and I'm only 26... It'll be pretty when I get older!). One day, I decided I would stop. I admit that I still did it every once in a while out of habit, but I tried to notice when that happened (as after a while, you just don't notice yourself doing it anymore) and I wouldn't do it on purpose. As time went by, I finally stopped. I may have the occasional cracking when my knuckles really bother me, just to relieve them, but it's now very rare (once a month? even less?) and I think I may be seeing improvements (my knuckles tend to hurt less frequently).
For all the people who say it's not bad for you, I think you are wrong (personal opinion ). Like Scott said, you're stretching a joint past its normal range of motion.