Al-Queda was never mentioned by Bin Ladin until after it had come up in his trial - in absentia - for the Nigerian embassy bombings (as kara said, the only way they could convict Bin Ladin was to use the old racketeering laws created to tackle the mafia, and that required an 'organisation').
IIRC the main testimony detailing the 'operation' of Al-Queda was from a defector who a) was paid several hundred thousand dollars for his testimony and b) had stolen money from Bin Ladin.
My understanding is that bin Ladin is simply a financier and fixer; he's rich, he probably has some names in his phone book, but he's not orchestrating any attacks - just wiring the money. IIRC the guy regarded as responsible for organizing 9/11 was Khalid Shaikh Mohammed. In fact, I believe many of the armed people seen in the various videos with Bin Ladin as his entourage were found to have been hired for that purpose (to be seen).
Not to say Islamic fundamentalist terrorism doesn't exist, of course; but it's politically expedient to depict it in the way Al-Qaeda allows. for one thing you have a Goldstein-esque figure of hate to blame, you have an identifiable target, and you have a mechanism to mobilise the population by presenting a seemingly credible threat to their existence. The truth is that these terrorists are organized in primarily independent small groups and cells, with shifting alliances and existing in shadow; it's not a case of cutting off the head to kill a snake. And because of this they will always exist - there's always going to be a lunatic fringe of humanity - the question is how to stop the 'normal' people who grow to sympathise and support them financially, logistically, or through engaging in acts of terror.
But these groups present a minimal threat to society compared to what they are portrayed as (under the guise of Al-Queda) - even despite todays tragedy, the vast likelihood is that we will never be within 100 miles of an attack, let alone caught in one.
I'd suggest looking for a copy of the BBC documentary 'The power of nightmares' (pt 3); it covers this in a lot of detail.
