Their different fates are telling. Clay Shirky grapples with the whole Wikileaks dynamic with his usual thoughtfulness here. I think he's onto something in his distinction between "international" and "global" media. International media - like the NYT or BBC - are based in a single country and are a product of its social and political norms and laws. Global media - like Wikileaks or Glenn Greenwald - belong nowhere and are institutionalized in nothing very solid. Classic Shirky analogy:
The LSD business is more global than the cocaine business, because coca leaves only grow in certain climates, but lysergic acid can be synthesized anywhere. Media is like this as well: The internet is more global than the telephone network, even though both systems can send data between any two points in the world. Similarly, Wikileaks is more global than the BBC or Al Jazeera; those organizations are very large, but they are international, with a home base as rooted in a particular place as a coca farmer is.
So governments can get at the sources of international media far more easily than they can global media:
Fans of game theory will recognize these conditions as those required for an iterated game of the Prisoner’s Dilemma, where the press exhibits self-restraint from short term defection against the US’s interests, in order to benefit from an amicable relationship with the government over the long haul. This is why the difference between the Times, as an international actor, and Wikileaks, as a global one, matters so much. Wikileaks does not have to play an iterated game of Prisoner’s Dilemma with the US. Not only is Wikileaks not housed in the US, it isn’t housed in any single other nation the US could complain to. They can defect at will.
I do think this is a paradigm shift, and a permanent one. The era of the Pentagon Papers is over. What will replace it we do not yet fully understand.