According to the Telegraph Ayman al-Zawahiri has taken control of al-Qaeda.

Osama bin Laden’s deputy has seized control of al-Qaeda and rebuilt the terror network into an organisation capable of launching complex terror attacks in Britain and America.
Intelligence officials have told The Sunday Telegraph that bin Laden has not chaired a meeting of al-Qaeda’s ruling shura, or council, in more than two years.
Instead, Ayman al-Zawahiri, bin Laden’s nominal number two, is credited with rebuilding the terror network since the Afghan war in 2001.
Intelligence sources in Washington have revealed that Western spy chiefs were recently forced to revise dramatically their view that al-Qaeda was so depleted that it was little more than a cheerleader for extremists.
Instead, British and American intelligence agencies believe that a network of terrorist cells, funded, controlled and supported by al-Qaeda’s central command, based in the lawless tribal areas of Pakistan, is in place again.

(via)
It shouldn’t surprise us that al-Qaeda survives our attempts to destroy them. They are a lot more cunning than we realize. The Looming Tower author, Lawrence Wright on the resurgence of al-Qaeda (from an interview on the Hugh Hewitt Show):

What it is the state of al-Qaeda six years after the attack on 9-11?
LW: Well, it’s a mixed report. You know, al Qaeda central has been, to some extent, reduced, isolated. It’s been unable to accomplish many of its major goals, especially capturing a Muslim country, and restoring the caliphate, and creating a kind of theocratic law. That it’s failed to do. But on the other hand, essentially after November, December, 2001, after the Tora Bora battle, al Qaeda was pretty much a zombie. It was over. The war on terror was at an end, and it’s been amazing to see how that organization has been able to reconstitute itself. It’s now deeply rooted in a lot of countries where it wasn’t present before. The banner of al Qaeda has been taken up by a lot of disaffected young Muslims around the world who hadn’t been interested in it before. So on balance, I think it’s as dangerous as it was before 9/11, but in different ways.
[…]
HH: Is the anger towards Bush in this most recent document the fact that the one thing he thought he knew best about the West has just proven not to be the case?
LW: No, I think that he is frustrated that we’re still in Iraq. And honestly, Hugh, there’s a…I think al Qaeda’s a little frustrated in Iraq as well, you know, they’re still in Iraq. That’s where al Qaeda’s preoccupied, and where it’s been pouring all of its resources in, and it doesn’t have much to show for it, either. It’s been frankly a draw. Al Qaeda’s in a great public relations situation, whereas if we withdraw, then they can say that they won, and that they defeated the other superpower. And if we stay, then Iraq is still a beacon for disaffected jihadis who want to go join the war. So they are in an enviable position, but really, they haven’t accomplished what they hope to do in Iraq.