To fan the flames of paranoia:
There were people on a flight which never made it back to an airport for a safe landing. Those people are gone. If we are to believe that no Flight 77 crashed into the Pentagon, it is possible that the flight was shot down - possibly the fear of it crashing into the White House prompted the shoot down call. Then, to cover up the shoot down, a missle/unmaned plane is sent to hit the Pentagon.
One piece of information I haven't seen here is that the area of the Pentagon that was hit was basically uninhabited due to renovations that had been going on for quite some time. Additionally, according to
this page, a large number of rescue and fire vehicles "just happened" to be very close to the Pentagon for a large building fire that "just happened" to go out moments before the Pentagon crash. (That page also has reports of a C-130 plane following Flight 77 as well as Flight 92.)