One of the most important facts that convinced me that JFK's assassination was an intelligence op is the alteration of his parade route to include Houston and Elm streets, because the shots from the office buildings in the area (and grassy knoll) would have been impossible without that change, and only the most senior national security officials would have the authority to alter the parade route.
Similarly, one of the major facts that convinced me that Bush did 9/11 is the presence of the NORAD drills (documented by Michael C. Ruppert). The drills were about intercepting hijacked airplanes that were being piloted into skyscrapers, and they were moved to the date of 9/11 from their original schedule. The confusion created by the drills that morning made the attacks possible, and Osama bin Laden did not have the authority to schedule those drills.