As an example of the sort of silly conspiracy-mongering George Monbiot was talking about in his article in the Guardian on Tuesday (which I linked), here is a reply to it (third letter down), which was published in the newspaper yesterday:
What if the "official" account of what happened on 9/11 is false? What if, in fact, it's a lie, and a big one at that, complete with corporate/media/propaganda cover-up? Without backing from the media the story wouldn't fly. What would that make this "war on terror"? A fraud? Since when do steel buildings freefall to the ground, like the World Trade Centre? Ever watched the video of it coming down? They didn't play it much on CNN or NBC. Ever wonder why? Because it's the smoking gun of the whole thing. It's proof because it's an obvious controlled demolition, which we all know takes weeks of planning, hence, foreknowledge of the attack, which means, an inside job.
The collapse of the towers was played, over and over again, on British TV, and it seemed obvious that a building would come down if a part was blown away far enough from the top, causing the top few storeys to crash down because what was holding them up had weakened from the heat and been taken away altogether by the impact. However, precisely because controlled demolitions take time and are invariably done after all the fixtures and fittings have been removed, and because there are not so many people in the controlled demolition industry that the government could find enough of them willing to take out two large buildings and neither tip off the WTC management, someone close to the workers or the local media in advance nor to talk to anyone about it afterwards, it is simply not possible for it to have been a controlled demolition.

I don't believe most of the conspiracy theories, but I don't accept the official story at face value either.
The whole statement about "pulling" WTC7 is what really throws things off for me. That, and the suspicious trading activity the day before. There are other anomalies, but those two confuse me the most.
What bothers me is how the ludicrous theories will be packaged together with the more reasonable ones, making the whole "truth movement" seem like a joke, populated mostly by some fairly wacky people. There is merit in a lot of the research, but it's offset by the absurdities some people believe.
I don't think anyone has all the answers, but I do think people need to realize how many questions still remain.
As-salamu 'alaykum,
While there are contradictions in the official version of events...as there often are in other less catastrophic events, I know that a conspiracy on such a wide scale couldn't be kept a secret. Heck, the U.S. government in general and the Pentagon in particular already leak like a sieve when it comes to secrets...much less the media.
I agree with Faraz. Conflating some of the very real and unanswered questions around 9/11 with the theories Rense.com-style cranks achieves nothing in the search for the truth.
If we are to identify a uniquely-muslim problem with conspiracy, then the finger of derision ought to equally point at the victims too:
A recent Scripps Howard/Ohio University poll of 1,010 Americans found that 36 percent suspect the U.S. government promoted the attacks or intentionally sat on its hands. Sixteen percent believe explosives brought down the towers. Twelve percent believe a cruise missile hit the Pentagon.
Every time I start to get a little comfortable with the official account, something else inevitably crops up that makes me think "hmmm":
http://english.aljazeera.net/NR/exeres/E07CA9CE-DF4A-4A74-A800-81751CC9D828.htm
We are being presented with an assortment of lies - some of them with more worth than others.