David Post has an excellent analysis of the Grokster decision over at Volokh. From what he suggests, Grokster, Moebius and Kazaa are all going down, as there is little to recommend them other than copyright infringement. However, there are a range of file transfer systems, and it's not entirely clear how they fall out.
Case 1: FTP -- File Transfer Protocol. Clearly FTP can be (and has been) used for transferring illegal files. But it was designed simply to allow basic file transfer over the Internet -- web site posting generally uses FTP -- and has never been marketed for any illegal purpose. Status: unaffected.
Case 2: Torrent. This is a tool which is useful only for sending large, well-distributed files. While much of the use has been video (audio files are too small), and particularly television shows and porn, it is also the method of choice for transmitting Linux distributions and other large public domain files. There is substantial utility and non-infringing use here. Status: the dividing line?
Case 3: eMule. This is a cross between torrents and Grokster, involving links of private networks hosting various files. Since nearly all content on eMule networks is copyrighted, this looks like it goes the same way as Grokster, with the possible exception of "intent" issues. Status: probable loser.
One question that hasn't been asked: Is the lack of non-infringing content simply a matter of choice, or is it a fallout of 95-year copyright terms? How much audio and video is there in the world not under copyright? If a service has a higher than-random percentage of non-infringing work, is it OK? If not, what is the criterion? Just asking.