I can't say...I wish I could say I completely disbelieved that there was anything shady going on during 9/11, but I can't. I don't necessarily believe anything beyond the stated explanation did happen, but I'm also not willing to say "no, that's how it was".
I certainly think that the 9/11 hijackers were who the government say they were, and that they did what the government said they did. I certainly think they trained with the Taliban under Khalid Sheikh Mohammed in Afghanistan, and that Osama bin Laden was behind the attack.
What I'm less sure about is whether or not there was something shady going on with the CIA. They're not particularly known for above-board tactics anyway, and with regard to the Middle East their history is rotten if not incorrigibly criminal. There was the Mossadegh coup in 1948, and the very covert support of Saddam Hussein from 1960 to 1990 while he used the same tactics against Communists and Iranians that we eventually invaded him for the first time for using against the Kurds, among other abuses. We actually supported Saddam in the Iran-Iraq War of the 1980s. There's also really been a paramilitary black-ops war going on in various places, Iraq included, between the CIA and the Iranian theocracy (who as we are now seeing are just as big a bunch of shady assholes as well) for some time.
Do I think the CIA orchestrated flying planes into buildings? No. But it's not beyond me to think that somebody neoconservative, high up in the command structure, might have had better intelligence than what they stated, and simply decided that "for the greater good" they had to allow some sort of massive incoming terrorist attack to actually strike the United States in order to rally support and power for the neoconservative planned RMA (the so-called revolution in military affairs). It wouldn't be the first time that a "to save the village we had to burn the village" mentality had taken root at high levels of our government. The Project for a New American Century - the thinktank/policy project that elevated most neoconservatives to power, there's a list of signatories somewhere - had a line in it that said the the RMA would be difficult to institute unless there was another event the size of Pearl Harbor. That's certainly an unfortunate line for them to have in the document.
I doubt many people were in on it, if they did "let it happen" - not the first time that particular thought has been advanced in the national discussion, but that level of high treason is hard to keep under wraps for long. Still, it just seems suspicious to me that they knew the identities of every hijacker within something like a few hours after the attacks, and other details that I remember reading about that seemed odd which I can't recall at present.
And the attitude of the later war declarations just felt...wrong. I don't know any other way to put it. Feelings aren't facts, but the attitude of the Republicans and Bush in declaring that war almost seemed...self-congratulatory in some ways. Bush was smiling and seemed almost happy, which struck me as the wrong tone for someone to take when his country was about to war - but, that could easily have been his personality, too, since he seemed to see this conflict as some sort of divinely appointed mission to cleanse the Middle East, with himself in the role of the gallant hero.
Anyway, do I think "they did it"? No, not really. But, much as it pains me to say this, I would not be entirely caught off guard it turned out that there were a few of the "save the village burn the village" types involved in the investigations and intelligence and keeping a low profile at higher levels somewhere.