Every morning I get out of bed and my knees and ankles pop constantly. Is that good or bad? Should I stop popping them?

No pain, no problem. We used to think that popping our knuckles, neck, back etc.. Caused arthritis. However, there is no evidence of causal relationship has been found until this time. It is indeed a habit and once formed, the joints "feel the need to pop" intermittently. As long as it does not cause pain while doing it..Enjoy the popping. If u don't like to hear the pop, don't do it..It will stop with time. Good luck.
Mine do too! I have frequent "popping" in my ankles, but it is benign. I do serious mountain biking, lift weights and never had a problem with ankle pain or arthritis! (minus the several sprains I have \had, albeit unrelated!).