This is excerpted from a long discussion of the process of analyzing terrorist networks, written by intel analyst Dennis Pluchinsky, in the Washington Times. If you're interested in the mechanics of the process it will make a good read. This paragraph deals with what happens to al-Qaeda...
Be aware that assessing al Qaeda threats today is more difficult. The pre-September 11 al Qaeda no longer exists. It has most likely metamorphosed into a new structure with different characteristics, tendencies, procedures, communication codes, false documents, membership, command and control, travel methods and financial channels. It is quite possible that al Qaeda may eventually transform itself into a "leaderless resistance" movement like the Earth Liberation Front or the defunct Revolutionary Cells in Germany. Al Qaeda could become amorphous, with no structure, hierarchy, central headquarters, or group dynamics. It evolves into an ideal that provides, via Web sites, CDs, videotapes, manuals and publications, the ideological framework and training for adherents. Islamic extremists around the globe could then decide if they want to further the movement by setting up small, local, autonomous cells to carry out attacks consistent with the ideological framework. In this scenario, al Qaeda is no longer called "the base" but the "nexus."
We've already seen that (a part) of al-Qaeda has assumed a new name â Fath e-Islam â and probably new leadership. This is the bunch that's reported to have moved back to Afghanistan and is allied with the Talibs and Hekmatyar's Secret Army of Doom. My guess would be that the Secret Army of Doom is built on a base of Hekmatyar's Hezb e-Islami, with a Taliban and an al-Qaeda/Fath e-Islam wing. The jihadis claim Zawahiri (or his ghost) is the Bad Guy in charge. I think it's Hekmatyar, with casual support from Iran.
It looks like there's also another functioning wing of al-Qaeda that's headquartered in Karachi, where the coppers just shot it out with the Bad Guys today. Ramzi bin al-Shibh claims to be in charge of the military shura of this bunch. Perhaps it's the one Binny's kid's "in charge" of. These are the guys who'll be allied with Harkatul Mujaheddin al-Alaami — or vice versa. Ultimate control of this bunch will be contested by the Pak fundos.
Those are two of the al-Qaeda successors that take form through a heavy mist of open-source. The active intel guys will have better information, so we can expect that if we can see a hazy outline, they can see some detail.
I think Pluchinsky has a very good point in that (a wing of) al-Qaeda could become simply a clearing house for "an ideal that provides, via Web sites, CDs, videotapes, manuals and publications, the ideological framework and training for adherents." That's not providing leadership, though; it's running web-based pep rallies. It's also not providing funding, training, and specialist support, so it results in a lot less effective organization. Pluchinsky thinks that if we stay the current course, al-Qaeda will be neutralized as a threat within four years. I think he's right. But I also think that the al-Qaeda remnants will be subsumed into the local terror machines, strengthening them. That's the more incentive not to stop whacking them as hard and as often as we can. 
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