Daniel Preece makes a good point…
Not to be picky, but there is no "non-conspiracy" theory about 9/11. The official Bush explanation is itself a massive conspiracy theory, involving dozens (or more) of extremist Muslim plotters spread from the U.S. halfway across the world to Afghanistan.
I point this out because some people use the phrase "conspiracy theory" merely as a label for explanations they don't like. This is dangerous to encourage, because it predisposes some people to disregard unpleasant explanations out of hand. And given the truth about the Boston Tea Party, the sinking of the Maine, and the Gulf of Tonkin incident (to list a few), we should keep a healthy skepticism regarding "official" explanations.
You're right. There are real conspiracies in this world and I certainly would never believe anything just because the voices that comprise "the government" at some point in time asserted it. On the other hand, I also don't give extra points to any theory just because it wasn't the official explanation. I think some people do, especially when the official version is of no use to them in their personal campaigns. Anyway, I'll try to be more precise about this in the future.