Popular Mechanics has a very readable debunking of many of the most prevalent 9/11 conspiracies. I am sure conspiracy theorists will generally respond to most of the scientists quoted with the all-encompassing "they're in on it!" Once you get so many people giving evidence that the conspiracies are incorrect, you drive the conspiracy into the realm of Meyer's Law:
When the same set of facts can be explained equally well by
- A massive conspiracy coordinated without a single leak between hundreds or even thousands of people -OR -
- Sustained stupidity, ignorance and/or incompetence
In this case, the word stupidity is unfair. The 9/11 attacks fall into the category of the "unimagined". Frank Borman (as portrayed in the awesome mini-series "From the Earth to the Moon", I have not been able to find out if they used his actual words) is speaking to a committee hearing on the Apollo 1 fire that killed three astronauts. Under intense scrutiny for a set of conditions that in retrospect seemed ridiculously unsafe, Borman described the problem as "a failure of imagination".
In this case, for example, conspiracy theorists ask why no military plane intercepted the aircraft. First, I would argue that without any prior precedent, no military commander or politician would have the cajones to shoot down a planeload of innocents on a commercial airliner (now THAT would be conspiracy fodder, had it happened). Second, though, the article quotes a number of military commanders to say that the US didn't really have the radar coverage or aircraft patrols in place to intercept an airplane attacking from within the country - everyone previously imagined the threat to come from outside our borders, and that is how our defenses were arrayed.
Anyway, read the who article - it is an entertaining roundup of conspiracy theories (people do have good imaginations) and a well-argued debunking of them. (via Instapundit)