Eric Lichtblau of the NY Times broke the story over the warrantless wiretapping (he has a new book out about this).
The Times also uncovered the recent story about the pentagon feeding propaganda to military "experts" who then acted as shills on TV. Their conflict of interest was never revealed (most have business relationships with military contractors).
On the web I only know of one site seriously involved in digging out such stories: TalkingPointsMemo.com and their spinoff TPMmuckraker.
It's TV and radio that have abdicated their roles as investigative reporters. A combination of business interests (such as military contractor GE owning NBC) and the need to stay on the good side of government so that their broadcast licenses and tax breaks are not endangered keeps them from doing real "journalism".
For all the talk about the internet, the bulk of it still consists of people citing work done by the traditional media. Where did the story at the top of this thread come from - a press release. Policies not Politics ---- Daily Landscape
A little bit of muckraking may still be done (in the New York Times), but its results are now being buried instead of pressed to their logical conclusions, as in former times when the media were still healthy and functioning watchdogs. It's no wonder that Americans are disgusted with the mainstream media and deserting the MSM in droves, and the mainstream media have no one to blame for it except themselves.