Seems like there is (once again) more conclusive evidence that cracking your knuckles is actually not bad for you, nor does it cause any sort of arthritis:
In fact, there was no difference in the prevalence of osteoarthritis between those who did or did not crack their knuckles.
The article also explains what's actually happening when you crack your knuckles, which is rather interesting, if you didn't already know:
Whichever method is used, the noise is created in the same manner. The space between the joints increases, causing the gases dissolved in the synovial fluid bathing the joint to form microscopic bubbles. These bubbles merge into large bubbles which then get popped by additional fluid which rushes in to fill the enlarged space.
Once the joints have been cracked they can’t be cracked again for about fifteen minutes. This gives the space in the joint time to return to its normal size and for more gases to dissolve in the fluid, ready to form bubbles which can then pop all over again.