While much of that site seems to be crack-pot-esque, There are some interesting questions to it. Of course, there's fairly obvious reasons that the Bush administration doesn't want any more investigation into it than possible; it would certainly cost the Republican party any chance of possessing the presidency for at least 8 years. (Very few people actually think Clinton could have done anything, and was so remote from the events, he wouldn't be harmed).
However, the question of how the towers might have collapsed is an interesting one. Here's and article that tries to calculate how much energy the explosion might have generated, compared to how much would've been needed to cause true structural damage:
http://hawaii.indymedia.org/news/2003/07/3248_comment.php
I also looked through the blueprints for the buildings a few months after 9/11, and I noted that the strength of the structure
did not primarily rely on the exterior walls; they only provided about 40% of the support for
each indiviudal floor. Thus, it would have made sense for the floors to eventually "break away", and slide out of the building. However, the main structure relied on an extremely heavy concrete core over 40' wide, that was reinforced with steel. It's unlikely that flames, even in the thousands of degrees, would have caused serious damage to it;
the core was designed to protect the building against collision by massive jets, such as the 747 of the day. This leaves me a bit puzzled as to how the towers perfectly collapsed, and without
destroying a single building outside of the WTC complex (though a few were severly damaged). I theorize that perhaps the terrorists might have taken measures beforehand to ensure the destruction of the buildings; planting explosives might have been a possiblity, but would have required some very clever use of them. However, I don't think that it is possible to underestimate Osama Bin Laden's skill with explosives, so that remains a possibility; it would be an even more embarassing security failrure for the US.