Also, there's the obvious, cynical "cui bono?" point. The government is one of the few entities that could reasonably be said to have benefitted from the attacks (expanded power, pretense for war, &c.), so if you start with the assumption that the "official story" is wrong the government would be the next most plausible culprit.
The argument used is much more applicable to creationist arguments of the form "evolution has this flaw, ergo god exists".
I think that should be 'pretext for war', not 'pretense for war'.
(Since there didn't seem to be one for this month, and I just ran across a nice quote.)
A monthly thread for posting any interesting rationality-related quotes you've seen recently on the Internet, or had stored in your quotesfile for ages.