I came up with one once. The theory was inspired by the 'backup, backup' theory advocated by someone with a certain assassinated US president's name as a screen name that says that the government just let KSM believe he came up with and implemented the 9/11 attacks so that the people who run the government, the arms and oil industries, could make money off the resulting war(s).
My theory, which has the same amount of evidence as the above one, is that a group of Truthers learned about KSM's plan, and encouraged it. They laid out ways to sabotage documents in order to support the terrorists, and bring up 'questions' that they can later then tie back to the government, the arms industry, and the oil industry (they gave up trying to tie it to the Jews). This would let them attack those groups, and be hailed as heroes. The problem is that, being ignorant, scientifically illiterate paranoids, they didn't tie the attacks to these groups very well. So they let, and in fact aided the 9/11 attacks, but failed to gain anything from it other than the hate of the vast majority of people.
Again, it has just as much evidence as the first theory. Of course I don't advocate my theory, but just use it to point out the faulty reasoning of 'they profited, therefore they did' idiocy.