The war on terror has led to the development of some unique tactics, derived from FBI operations against organized crime, and Israeli techniques for crippling Palestinian terrorist operations. These counter-terror tactics take advantage of the fact that Islamic terrorists are dominated by Arabs, and Arab terrorists share certain cultural habits common throughout the Middle East. The biggest weaknesses being exploited are the corruption and paranoia. Arab societies have a far more easy going attitude towards corruption, especially diverting (to personal use) a portion of funds you are entrusted with. Much of the email and letters seized from terrorists touches on money problems, either that there isn't enough cash, or that some of it is missing and it's not my fault.
Money is key to running a successful terror campaign. This is often overlooked by the media reporting on how terrorists work. But captured documents, and captured terrorists, make it clear that money is a major issue. Not that terrorists are mercenaries, although some appear to be, but people have to live. Not all terrorists are young, single males looking for a suicide mission. Many are older, married men with wives and children to take care of. You need these older guys to make the organization work, and they fellows need a steady income. One thing that made al Qaeda such a large and relatively effective terrorist organization was it's attention to mundane things like payrolls and benefits.
By 2002, it was clear that the best way to hurt al Qaeda was to cut off the supply of money. Lots of cash, and signs of funds stashed at foreign banks, or held by certain individual, were found in Afghanistan in late 2001. These sources were run down as quickly as possible. But there were some sources of cash that were not vulnerable until 2003.
Since the 1990s, much had been learned about how Islamic terrorists used Islamic charities and wealthy Middle Eastern Moslems to get money for the cause. After September 11, 2001, these sources were gone after aggressively, but many of the donors were protected by personal connections in their home countries. Saudi Arabia and the other Gulf States only stepped up their efforts to cut off this cash after Iraq was invaded in 2003. The violent response of Islamic terrorists, throughout the Middle East, to the Iraq operation, made it clear that cutting off local support for the terrorists was simply an act of self-preservation. The Iraq invasion inflamed the many Islamic radicals living in the region to do what they had not done before, make attacks in their home countries. This was usually avoided by terrorists, because such attacks turned family and neighbors against the terrorists. It's easy to cheer terrorism in other countries, but it becomes hard when the bombs go off down the street.
Getting agents into al Qaeda is a lot more difficult, as the terrorists depend on personal recommendations when recruiting senior members. The Internet has proved a good way to get around this, and build a reputation and "legend" (convincing back story) inexpensively, and with much less risk to field agents. In any event, getting your own people into a diffuse organization like al Qaeda (and its many affiliates) is a long term operation. In the meantime, as the Israelis have demonstrated, it's much easier to find, and exploit, weak links in the existing enemy organization.
While shutting down the terrorist bank accounts, or actually seizing cash, some more experienced investigators realized this provided an opportunity to cause additional damage to terrorist cells, especially if the guy in charge of the money was not caught. All you had to do is not give any publicity about the money seizure. Keep it quiet. There was a good chance that the terrorist responsible for the money would not be believed when he told his superiors that the money was seized, or otherwise disappeared as the result of counter-terrorist operations. Captured al Qaeda mail had disclosed a lot of angry queries to subordinates about what happened to money the underlings had been given. There were accusations of theft or misappropriation of funds, some of them later found to be accurate. After 2001, al Qaeda had less reliable communications, and fewer troubleshooters they could dispatch to branch offices, to clear up problems with missing money. Paranoia and nervousness were on the increase because of the American, and world, response to 911.
The increased tension in post-911 al Qaeda cells provided other opportunities as well. Some al Qaeda members now wanted out, but the closer you were to the core members, the more difficult it was to get out. So counter-terrorism officials made it easier for terrorists to leave the business. While not exactly a witness protection program, arrangements could be made to move the repentant, or just burned out, bad guys to safety. With so many Moslems communities in the West, this is a lot easier. In some cases, the terrorists were turned (into double agents), and provided information to their handlers.
Captured terrorists also provided other opportunities. After 911, and even with the Internet, al Qaeda communications were poor, as was their intelligence work. Bottom line was, most al Qaeda members were never sure if a fellow terrorists had been killed in action, captured or defected. Because of this, even dead terrorists could be useful to counter-terrorist operators. You could keep a dead terrorist "alive" on the Internet for a while, or in the minds of other terrorists being interrogated at places like Guantanamo. And then there was the classic interrogation trick, threatening to frame a terrorist as an informer, and release him. If done well, this was a formidable weapon, for it threatened the terrorist with a fate worse than death, to be tagged as a traitor.
It will be years, maybe decades, before all the details of these operations become public. But that's how these operations run, in the shadows and on the fringe of reality.