I crack my knuckles often and they are the same they always were. I used to crack my neck quite forcefully but I stopped. In the case of my neck it appeared to be progressively getting worse, and after stopping my neck generally feels less strained. Now my neck does not crack so easily.
I had a complimentary adjustment by a chiropractor once. When his work caused pops and snaps he said that this stimulated the nerves and released tension. This follows my experience in general, as long as you are not straining it at the same time. Sometimes popping a joint is actually dislocating it and setting up further tension. I'm sure we all the have experience of putting our back or neck out this way.
I found that turning my head all the way left and right and applying "stretching" pressure often resulted in pops, and would calm me and give me a more restful sleep. The same is true for twisting all the way around so my back stretches a bit. At the same time doing this too regularly or as a nervous habit will result in straining the muscles and structures that keep the joints in proper alignment, and so they may go out of alignment more often and be sore. I am only speaking from experience.
My mother uses muscle relaxants to help when her neck or back goes out. So clearly tension and stress can play a factor here. Cracking a joint while those muscles are in tension (which is usually true if it is a nervous habit) may stimulate the nerves to partly release the stress but will also strain the muscle creating a worse condition than before.
So based on my experience, cracking joints is okay as long as it's not straining, and it's not a nervous habit.