I looked at some of the conspiracy videos and pages on the net a while after 9/11. While there are one or two tiny weeny pieces of info that bear slightly more than a passing thought, most of the conclusions they come up with are total rubbish. They exhibit a complete misunderstanding of flight control, explosives and flying ability.
For instance they suggest that the 757 that hit the pentagon couldn't have done the manoeuvre that it did - well as a 757 pilot I can tell you that it can - although I've never actually done such a thing. I have however flown an aircraft with the same rate of descent they said was "impossible" and turned in a similar radius, both in the aircraft and the sim.
The only piece of 9/11 myth that bears the slightest thought is the damage to the pentagon - I would have expected more but then I wouldn't be surprised if the pentagon was built much stronger than your average building. At the time it was reported as a truck bomb, then revised to an aircraft. This is the only bit that bears a bit of thought - and I'm not saying the conspiracy people are right - but I would ignore the rest of it as complete supposition, misunderstanding and hype.