Ron Unz has some well considered articles up on the Kennedy assassination. He sees Johnson as the likely culprit which a simple "cui bono" and Occam's Razor, on first blush, tends to support. But did Johnson really have the machinery at his disposal to execute on something like this, or was he just a willing opportunist who found himself in the right place at the right time?
Conservatives like Unz tend to see all the progressive portraits of John Kennedy as hagiography and discount the degree to which he may have internalized the jaded idealism of FDR in a "post colonial" ambition for America's post war foreign policy. If, on the other hand, you take the portraits painted by Bill Moyers or David Talbot of Kennedy's intentions in his very short Presidency, and compare them to those of our current president, in his second year in office, and compare the Kennedy they portray to the institutional biases Kennedy was up against, you might arrive at a different conclusion to "cui bono", and with that different suspects.
De Gualle for one saw the Kennedy assassination as a political statement by the imperial forces entrenching themselves across his career in US policy circles, he said so explicitly in his memories. Allan Dulles is my prime suspect, having motive, means and opportunity, in fact this kind of thing is exactly what he built his career on. Talbot's biography of him, "The Devil's Chess Board", lays out from the old spooks personal calendar the array of exotic criminals and hit men he met with in the months prior to the event. Including some interesting correspondence with Kennedy's Secretary of Treasury, the boss for Kennedy's personal security escort which failed so profoundly on that day in 1963.
Dulles was forcibly retired by Kennedy who had openly disagreed with the very colonial foreign policy Dulles, like his late brother J. F. Dulles, was deeply committed to. The Dulles brothers, before the war had arranged for US and German industrial secrets to be shared between the cross shareholders on boards of the likes of Union Carbide and AG Farben or Ford and Daimler, who were all clients the brothers represented at Sullivan and Cromwell. Truman considered Allan's activities in Switzerland, where he had tried to arrange a separate peace with the Nazis in a piece of monstrously ambitious insubordination to FDR's express policy of unconditional surrender, treasonous. It was the political intricacy of Dulles' embedment at the head of the CIA that prevented Truman from acting on this.
Further, Talbot catalogues the rather long standing and complex relationship of Lee Harvy Oswald to Allan Dulles and the prior use that had been made of him in thwarting Eisenhower's intent to thaw relations with Krushchev. The book is well worth the read. Suffice it to say that Allan Dulles was a past master of insubordination to Presidents, a master of conspiratorial organization and a serial assassin. If one takes the word of those closest to him, Kennedy had every intention of re-grounding Cold War US policy in FDR's anti-colonial, anti imperialist (he had fenced with both Churchill and DeGaul on this subject before and with Churchill after Yalta) vision.
Dulles was an unashamed American Imperialist and a Nazi sympathizer. He didn't share their racial hatreds, but certainly their sense of racial superiority. He facilitated the post war escape of many of the richest Nazis who in all likelihood funded Dulles secret operations up to and beyond the time he left the CIA at the young, soon to be dead Presidents discretion. Not only did he talk to Douglas Dillon, former investment banker and Secretary of Treasury immediately before and after the assassination, but he managed to place himself at the head of the Warren Commission investigating the crime. It was at about this time that the CIA spread the meme "conspiracy theorist" to denigrate anyone who might look to closely at this.