Seems that the NSA turned on persistent cookies in violation of a Federal rule that proscribes them unless there is a "compelling need." Of course there are a few people turning this into some kind of conspiracy or sign of gross incompetence. Of course, none of these people are concerned about the millions of other Web sites that use cookie. Bizzare.
Jeff Jarvis also comments on this story and how the media thinks they got some huge scoop here. Here's a white paper (PDF) that I wrote when I was Utah CIO about cookies and privacy. We were having our own little debates with people (on my staff) telling the media they were "programs" and other silly ideas. I wrote the white paper to try and explain what cookies are and how they relate to privacy.