The Pentagon attack has arguably attracted more conspiracy-related debate than any other 9/11 issue. Here’s a sample of sites covering just some of the arguments, and an official report or two for further reading.
Flight 77, or at least a large plane may have hit the Pentagon
JoŽl van der Reijden - Why the No-757 Crowd is Making an Ass out of Itself
Oilempire - the "Pentagon missile" hoax - the more important disinfo about 9/11 complicity (also see http://www.oilempire.us/pentagon-truth.html)
Jean-Pierre Desmoulins - Pentagon 2001 / 9 / 11 : the fraud !
911Research - The Pentagon No 757 Crash Theory: Booby Trap for 9/11 Skeptics
John Judge - The Pentagon Attach and American Airlines Flight 77
QuestionsQuestions - New turns in the 9/11 Pentagon debate
Pentgon engine debris investigation - analysing “two key pieces of wreckage photographed at the Pentagon”
Major doubts over the official Pentagon story
Killtown - Did Flight 77 really crash into the Pentagon?
Physics911 - The Missing Wings
Pentagon Strike - famed Flash movie on "no plane at the Pentagon" theories
APFN - We are Not saying, that was was NO plane, Flight 77 that crashed into the Pentagon. We are saying, Where IS Flight 77, at the CRASH SITE?
911-strike.com - The Five-Sided Fantasy Island
In Plane Site - Why were America and the world never shown the video and photographs of the Pentagon, BEFORE the outer wall had collapsed showing only one 16 ft. hole...
Pentagon-specific photos (see general photos here)
Steve Riskus - A collection of photos taken moments after the Pentagon was hit
Security camera footage - Photos obtained by CNN apparently show the fireball resulting from the Pentagon impact
US Defence Department - Photos of the Pentagon crash aftermath
Defence Visual Information Centre - Another US Government site. Search on keywords like American Airlines to get Pentagon photos
ACSE - The Pentagon Building Performance Report, by the American Society of Civil Engineers
Arlington County - "After-Action report on the response to the September 11 terrorist attack on the Pentagon". A sizeable PDF file (7+ MB) but one or two interesting eye-witness accounts, and lots of procedural detail on what happened locally after the attacks. Worth a look if you're interested in every detail.
Flight 77 Pentagon video - There’s barely any more than the previously released frames, but if you want to see them then they’re available in streaming format here. We also have them in downloadable form, both video 1 and video 2.
Flight77.info - Documenting the legal process to obtain government-held video recordings related to Flight 77 on 9/11
Mike J. Wilson’s 911 Report - This guy has built 3D computer models of Flight 77, the Pentagon and surrounding area, then run the plane through its final moments to see how that might have looked. Here’s an example of how he suggests Flight 77 would have looked, in comparison with the security camera footage (full-size image on his site):.
American Memory -- The September 11 2001 Documentary Project consists primarily of lengthy audio interviews with various people, giving their reaction to the attacks. Most have only social interest (people who only saw the events on TV), but others, particularly of people working at the Pentagon, are more interesting.