9/11 Conspiracy Theories (Not the pentagon plane)

We’ve beaten the pentagon plane thing to death here, and that’s not what I’m asking about, before you close the thread.
A friend of mine has recently been caught up in all this 9/11 conspiracy stuff that says that the US Government perpetrated the attacks. There’s all this “evidence” (and I use that term loosely) and “information” about our links to the pakistani ISI and other things.

Here’s the issue. I don’t believe him. I’m 99% sure he’s wrong, yet there’s not a single site out there refuting the “evidence” brought by all these sites about these theories. Maybe there is and it’s just dwarfed by these sites getting all the recognition, and if there is, please show it to me. If I get enough help here, I think I’ll try to maybe compile it all into one site.

If you know of anything that can help explain/rebut these, please do. If not… I’m scared I might go into believing this too, as nothing can explain them.

http://www.onlinejournal.org/Special_Reports/080703Chossudovsky/080703chossudovsky.html
http://www.globalresearch.ca/articles/CHO206A.html

Most of the conspiracy theory info leads to ties to the pakistani ISI (intelligence) and Mahmoud Ahmad, the cheif of intelligence. On 9/11, he was (allegedly?) having breakfast with Senator Bob Graham and Rep. Porter Goss. Mahmoud Ahmad had allegedly ordered the transfer of $100,000 to the presumed 9/11 ring-leader Mohamed Atta.

http://www.scoop.co.nz/stories/HL0208/S00085.htm
My friend is also big on some theory about how some of the hijackers had been training on a US Naval Base. This one seems interesting? It just doesn’t seem to be plausible that noone knows about this, or maybe it just doesn’t even matter and I’m being stupid.
http://www.ratical.org/ratville/CAH/AOPof911p11.html
http://www.madcowprod.com/issue31.html
Does anyone know of a site that contradicts these reports? As the smartest MB I know on the net, I’m sure someone here can help me out with trying to make sense of all this.

http://www.911myths.com/html/trained.html

Training foreign pilots is nothing shocking, and all we have is a very common Arabic name to connect the two locations.

Thanks! Too bad that site has nothing about the whole “Ahmad” thing. :-x It’s a great start though and talks about alot of the stuff he talks about. Glad to know most of it is BS.