This all seems very complex to me, and I can see why the courts are having problems with such issues. Should a company be required to track every bit of information that passes through its servers and workstations? My kneejerk reaction is, no, it shouldn't. First, it would be virtually impossible to manage from a sheer storage perspective. Second, does the government have an inherent authority to require the maintenance of such information? Can it, in fact, force private organizations to do its own investigative work?
Note that I'm not a fan of "privacy" as a catch-all to mask all sorts of otherwise illegal activities. Consider that this particular case concerns Torrentspy, a site that makes it easier to locate and download pirated intellectual property. Furthermore, I don't believe that "privacy" is any sort of Constitutional right, nor can it really be found anywhere in the Constitution.
Rather, I believe we have privacy with regard to our own property, such as our homes, cars, bodies, computers, etc. Once we put information out on the Internet, all bets are off. But the linked story does raise some interesting questions.