Al Qaeda is not a normal organization. In reality, al Qaeda is a collection of separate terrorist organizations with a lot of common goals, enemies and methods. They cooperate under the general advice and direction of al Qaeda leaders and technical experts. There is an "al Qaeda", but many of its members simultaneously belong to al Qaeda and other terrorist organizations. Al Qaeda didn't have a very efficient personnel department, but they left a lot of records behind in Afghanistan, and other places, that American intelligence agencies have used to reconstruct a personnel list (which they are not sharing with the media just yet.) That list, combined with interrogations of people picked up in Afghanistan and elsewhere, apparently provides some idea of how many al Qaeda fighters were lost, and where. Moreover, a number of the al Qaeda lads that made it out of Afghanistan, were found to have reconsidered their chosen profession. Some of these "retired" terrorists were apparently interrogated after they got home to Kuwait and Saudi Arabia. Local police, who spoke with the family members of the al Qaeda recruits, appear to have confirmed that many of these "retirees" are legit. There were defections like this even before US troops and JDAM bombs showed up, as Arab al Qaeda recruits were put off by the wild and primitive (to Arab eyes) Afghans and the grim goals of the al Qaeda organization.
But al Qaeda is still picking up new recruits, it just doesn't have as many training camps to evaluate and educate the new men. Most of the new people appear to be getting on-the-job training in whatever country they are recruited. Attempts to set up new camps in places like Indonesia, the Philippines, Yemen, Pakistan and Afghanistan have met with little success (although some have been established, for a while at least.)
Al Qaeda will be around for at least a generation. But by capturing the more capable leaders and hounding the organization wherever it attempts to establish training areas, the effectiveness of the organization can be reduced to near zero.