If I've said it once, I'll say it a million times: I think the Mob killed JFK, with the blessing of the intel community.
Why? Well, when you think about it, the U.S. government has never actually had a huge problem with the Mafia. It took one crusader who finally had to resort to tax evasion charges to nail Al Capone; no one was looking too hard for the guy, because organized crime is useful if you emphasize "organized." Solving crime becomes a lot easier when you always know who's responsible, and if it's not performed out in the open, we conduct periodic arrests to keep the books straight, and especially if we get a cut of the take, the government generally doesn't care.
(Frankly, organized crime has always kept the peace and even been fairly more progressive than the government, though often for selfish ends. Look at how they ran gay clubs back in the day; say what you will about the poor conditions and underhanded business tactics forced on them by society, but the O.G.s saw a business opportunity and provided the LGBT community with a much-needed haven at a time when the rest of the country was still hostile and unwelcoming. But I digress...)
Truth be told, we've made use of the Mob for our harder jobs on more than one occasion. Google "Operation Underworld" and "Operation Husky", to say nothing of the aforementioned-in-this-thread attempts to take out Castro and Greg "The Grim Reaper" Scarpa turning informer for the FBI and solving the fire-bombing of Vernon Dahmer in Mississippi with the help of pistol-whipping skills to the tune of 30 grand.
The Mob put money, muscle, and considerable influence into JFK's election at the instigation of his father, who they knew from way back as a bootlegger. They were led to believe that things would be the same as always, or even improve. And, though -- tellingly -- he never looked into voter fraud, RFK, who'd learned nothing from his old man about welshing on deals, was appointed to head the Justice Department and made fighting organized crime a priority. As Victor Navasky put it in his book, [italic]Kennedy Justice[/italic], "...ever since Prohibition... attorneys general have been ‘declaring war’ on organized crime, but Robert Kennedy was the first to fight one."
So they bit back. JFK found out a Dallas welcome only lasts about twelve seconds, and they ain't pretty. As he'd already pissed off other machinery in high places, machinery that wasn't upset to see him dead for reasons of their own but also didn't want to admit the Mob could take them out so swiftly and decisively with one blow, the nets descended and the cover-up began.
Jim Garrison says in the film [italic]JFK[/italic], "Could the mob change the parade route, or eliminate the protection for the President? Could the mob send Oswald to Russia and get him back? Get the FBI, the CIA, and the Dallas Police to mess up the investigation? Get the Warren Commission appointed to cover it up? Wreck the autopsy? Influence the national media to go to sleep?" No, they couldn't, not that some of that stuff happened to begin with. But the people who could do it were afraid of looking weak because they underestimated "scrappy thugs" who took out the big cheese and revealed just how fragile they were. And being afraid of looking weak is as American as apple pie.