According to this article by the John Hopkins Arthritis center there has been no evidence linking the habitual cracking of one's knuckles to joint damage such as arthritis. Alas they do state that some studies have found a connection between knuckle cracking and damage to the ligaments and tendons around the joint, though these seem to be rarer cases and not taken as wholly representative. Another negative side effect mentioned is strangely enough, a decrease in grip strength.
Despite the institute’s known reliability and reputation, this article did not include a works cited section. Though with a little digging I found this study in the National Library of Medicine that makes use of very similar verbiage. Considering that the article by the John Hopkins Institute states that “a study found”, singular, this is likely said study. Admittedly this is quite an old study haven come out in 1990, it’s reliable being in a peer reviewed medical library.
There is also the case of the Dr. Donald Unger who, as outlined by this BBC article, experimented on himself. He habitually cracked the knuckles on just one of his hands for 50 years. Later X-raying both his hands and finding no difference in arthritis between the one that was cracked twice daily and the hand that had ne’er been popped. Whilst it doesn’t have nearly the same sample size as the previous (300 individuals as opposed to one), him being a doctor (not to mention being a noble prize winner) in addition to the staggeringly long period of time the experiment ran for, gives it more than an air of legitimacy. It is also from what I could find, one of the most cited experiments regarding this subject area.
All that being said, if arthritis is your only concern, crack to your heart’s content, just know that, even if they’re rare, there are other risks.