Here's my argument in a simple deductive form because many have missed the point.
Premise one: One is unjustified in believing a conclusion if the methodology used to arrive at such a conclusion is deeply flawed.
Premise two: The methodology creationists use is deeply flawed.
Premise three: The methodology '9/11 truthers' use is similar to that of creationists.
Conslusion: One is unjustified in believing the conclusion of '9/11 truthers.'
One of the biggest strategies of both creationists and '9/11 truthers' is what I will call the 'house of cards strategy.' '9/11 truthers' and creationists envision accepted accounts of how the world is and what has happened in the past as a flimsy house of cards; if one part of the house is 'pulled out,' they believe that the accepted account completely fails and, of course, their version automatically wins out. This is a classic example of a false dichotomy in which two options are posed and if one is problematic, the flawed logic assumes, the other option automatically wins. As far as evolution and the accepted version of the narrative and happenings surrounding 9/11, it will be the case that there will be some errors in what was initially posited as truth - and this is inevitable. The errors, though, do not entail that the entire theory falls apart.
'9/11 truthers' and creationists love to cherry pick some accounts instead of looking at the whole picture. Creationists, for example, will point to Piltdown Man or Haeckel's Embyros (without, of course, looking for what the relevant experts have to say about these or performing a rudimentary Google search) and believe that this is enough reason to discount evolution.
'9/11 truthers' will say things like "The hijackers' names were not on the flight manifests" and conclude, of course, that "this is evidence of a lie." The earliest released information was, in fact, not manifests, but rather lists of the victims. The manifests were later released, but the '9/11 truthers' will not acknowledge that...and if they do, they offer ad hoc explanations to explain away the evidence which leads me into the next point...
Creationists and '9/11 Truthers,' when confronted with evidence that would dismiss their arguments, offer unfalsifiable/untestable explanations that are coupled with no evidence or very weak evidence. Creationists may say that fossils are just 'a test of faith.' '9/11 truthers' will say that the evidence is simply part of the conspiracy. In the case of photos of the hijackers, Big Dan notes that "You'd have to contact family members and get them to provide you with photos, right? Unless of course you had the photos in advance [...] There is NO WAY (emphasis his) - they would have withheld the complete list of alleged hijackers [sic] names until such time as they had tracked down every perfectly framed and in-focus head shot of every alleged hijacker." Why should we assume that fossils are a 'test of faith?' How can we possibly demonstrate this? Why assume that the evidence is part of the conspiracy?
Creationists and '9/11 truthers' both make inappropriate appeals to authority and assume, just because someone has some sort of title, that everything that person says is true regardless of what other relevant experts have to say who overwhelmingly disagree. Creationists appeal to people like Michael Behe who allege that systems must be intelligently designed because if one part of a system is removed, the system breaks down. '9/11 truthers' appeal to what ought to be called the poster-child of the inappropriate appeal to authority, ae911truth.org, for their information. The 'experts' are often speaking outside of their fields and do not offer peer-reviewed studies to supplement their ideas. The 'Architects and engineers for 9/11 truth' are speaking outside of their field when they are discussing controlled demolition. The controlled demolition experts have not come to a consensus stating that 9/11 was a controlled demolition...and those are the people we should listen to (and not just because they are experts on controlled demolitions, but rather because they are the best to interpret the evidence and present the evidence).
Creationists and '9/11 truthers' commit the informal logical fallacy known as the argument from ignorance. Both groups frequently use this pattern, championed by Bill O' Reilly, to supplement their arguments: this can't be explained, therefore conspiracy/God. Just because something can't be explained or is not explained does not mean that the creationist or '9/11 truther' is justified in asserting their claims.
The main narrative of the 9/11 conspiracy theorists is that the government and the media lie, have lied, and have participated in deception in the past. They reason, therefore, that since the media and government presented information regarding 9/11, it must be false. Creationists point to examples like Cold Fusion or paint scientists to be 'dogmatists' and therefore reason that scientists can not be trusted. Both camps posit non-sequiturs unjustifiably distrusting the sources of information (that are often quite unrelated or have nothing to do with what they are attacking).
While it is often a great idea to distrust patently unreliable sources of information such as World Net Daily, Conservapedia, or Life Site News, for example, the reasons for doing so should be quite obvious and rejecting such sources is acceptable. In the case of the government and media, it certainly is true that there has been deception and lies, but it simply doesn't follow that everything presented by the government and media (particularly information surrounding 9/11 is false). Similarly, attacking all of science or evolution by attacking certain scientists or trying to paint scientists as dogmatists is unjustified. One of the main goals of science is to reduce bias as much as possible, weed out bad ideas by scrutiny and peer review, and arrive at the best information possible. While some bad studies may be published, this doesn't mean that everything published should be dismissed.
Creationists and '9/11 truthers' commit the false cause fallacy. Creationists claim that evolution is part of a strategy to 'eliminate God' in the schools and 'promote atheism.' They look at the removal of school prayer, for example, and notice the increase of teaching of evolution in schools and reason that there is some sort of 'agenda' going on. '9/11 truthers' allege that 9/11 was some conspiracy by the Bush administration because of the increased militarism of the United States (namely Iraq and Afghanistan).'
Creationists and '9/11 truthers' create the illusion of controversy. Creationists allege that there is a great deal of controversy and that evolution is 'just a weak theory.' 'Organizations' such as the Discovery Institute try to make their side seem professional by asserting that there are 'creation scientists.' No significant amount of scientists, though, reject evolution despite various lists that creationists may accumulate. Similar to the creationists, '9/11 truthers' also present lists of people. Right on the front page of ae911truth.org, one of the first group of lines of text seen reads "1,601 verified architectural and engineering professionals and 13,342 other supporters have signed the petition demanding of Congress a truly independent investigation."
Truth is not a matter of popularity. When scientists reach a consensus, their ideas are not justified simply because there are so many people who accept them, but rather because the evidence warrants a consensus and because there is no reasonable doubt. While specifics or predictions made by the background theory might be questionable, the background theory itself does not suddenly become unjustified.
While I have not devoted a significant amount of time to study of the 9/11 attacks, I can spot fallacious thinking when I see it. Creationists and '9/11 truthers' commit very similar errors in thinking...not to mention the fact that much of the information they present has been discredited or 'answered' in various venues.