The body of conspiracy theory evidence in John F. Kennedy Jr.'s death is
overwhelming, if not outright mind-boggling. A wealth of data can be turned up to support almost any theory about what happened that fateful day in Dealey Plaza. But time and again, a small number of theories keep floating to the top of any discussion of Kennedy's assassination.
1. The CIA
Not long after the infamously failed Bay of Pigs Invasion, Kennedy told one of his confidantes that "Something very bad is going on within the CIA, and I want to know what it is. I want to shred the CIA into a thousand pieces and scatter them to the four winds."
Coincidentally, Kennedy's assassination marks an era when the CIA was heavily involved in the attempted assassination of various world leaders (including Castro). According to this theory, the CIA may have gotten a little assassination-happy, in an effort to protect itself. You can see how a shadowy CIA figurehead could justify the assassination of Kennedy as an effort to maintain the preserve the greater good which the CIA would be able to do, if it was not dismantled.
One item bolstering this theory is that the CIA did, unquestionably, continue to exist after Kennedy's death.
The CIA theory is linked to the "Three Tramps," three men who were questioned by police in the aftermath of Kennedy's assassination. These three men (E. Howard Hunt, Frank Sturgis, and Chauncey Holt) all had CIA connections, and were all present at Dealey Plaza without - according to some - reasonable explanations for attending.
2. The Mafia
The Mafia would have had good reason to want Kennedy dead, and no doubt was relieved when he was gone. Robert Kennedy had put a tremendous amount of pressure on Mafia interests, and at least one Mafia bigwig (Carlos Marcello) threatened to kill JFK in order to get to Bobby Kennedy, who was positioned to become Attorney General, and who was also openly working to quash the Mafia.
Out of all the organizations said to be gunning for JFK, the Mafia is perhaps the most plausible suspect. The Mafia is an organization which is literally dedicated to criminal acts, and which practically considers homicide just another day-to-day event.
(This theory merges with the theory in the #1 slot in a particularly baroque and unlikely way, combining to form a sub-theory in which the CIA hired the Mafia to assassinate Kennedy.)
3. Castro
It has been well established that, in the years before Kennedy's assassination, the CIA made several assassination attempts against Castro. (Each, seemingly, more asinine and bizarre than the last.) No surprise, then, that the Cuban leader should try to retaliate. It might be more surprising if he didn't, frankly.
This theory also has the benefit of leveraging one of the few things we know for sure about Lee Harvey Oswald, which is that he was a Communist sympathizer who suddenly came into a (for him) large sum of money not long before Kennedy's death. He set up his own branch of a pro-Castro organization in New Orleans, and could often be seen handing out pro-Castro leaflets around town.
On the down side, there is little evidence tying Castro directly to Oswald. If Kennedy's assassination was Castro-related, it seems most likely only in the sense of being the work of an insane, self-aggrandizing man who was desperate to curry the favor of any government (be it his own or another country's).