The history of several developing nations has had ocurrences of people who just "disappear", never to be found. Argentina comes to mind. In the 70s a tyrannical regime made people "disappear". No bodies were found, and people were left wondering "what gives?"
I think this is a different situation.
- in Chile and Argentina, everyone knew very well that the right-wing military death squads were kidnapping, torturing, and killing people, and that often the military "disposed" of the bodies afterward. For details, see Jacobo Timmerman's "Prisoner Without a Name, Cell Without a Number", an account of his kidnapping and imprisonment. President Carter's human rights advisor kept pestering the Argentine junta until they released Timmerman; Timmerman was a well-known journalist, but most of the victims were not famous.
- here we have a big airplane, carrying passengers who made cell phone calls describing the highjacking. One was the wife of the US Solicitor General.
- of conspiracies in general: it is hard to keep a secret, and harder with each conspirator you add. That's why isolated psychopaths can shoot people like McKinley, or JFK, or Martin Luther King, or Wallace, or John Lennon, or Reagan: having no ties to anyone, they are in less danger of being discovered before they act.
- with 9/11, it is clear that (a) Administration officials were paying attention to other threats. There were no Air Force jets patrolling the East Coast because the Soviets were no longer able to bomb us (b) airline high-jackers had always tried to fly to a neutral country and bargain the passengers against something...therefore, plane crews had been trained to put up no resistance, thus minimizing the risk to their passengers. People were trained for hostage situations; almost no one (except movie script-writers) had suggested that a terrorist might make an airliner into a flying bomb.
- Al Qeada found a tactic for which no one was prepared. There is evidence of all the normal amounts of government laziness, zeal, incompetence, mis-placed focus, agency information-hoarding, etc...but no conspiracy.
You ARE "They"! 
I knew it from day one! 
-- just goes to show how subjective 'conspiracies' are! (Which we have already ascertained YOU are behind them all!) 