There are a wide variety of good issues that the universities are trying to bring to the table before this situation gets even more out of hand than it already is.
MIT and Boston College have both filed suit alleging that the subpoenas violate the rights of students under the Family Educational Rights and Privacy Act, which provides additional privacy considerations for students and requires notification and appeal before providing information to third parties except under some very specific conditions.
Boston University has a different issue with the subpoenas. Their complaint is that the subpoenas should be filed in the local jurisdiction that they are being prosecuted in, instead of the Washington, DC District Court, as the RIAA has done. The EFF agrees with BU on this complaint and has stated that they feel a single nationwide clearinghouse for such subpoenas is an assault on civil liberties.
Of particular interest was a quote from an RIAA spokesperson who chided MIT and BC for not complying stating "We're disappointed that these universities have chosen to litigate this and thus denied us and other copyright holders the rights clearly granted to us by Congress." Interesting not because of their stance, but their willingness to use the word "rights" in a legal context, which certainly raises the hairs on the back of my neck about this issue. The congress may have (incorrectly) provided them with the privilege of issuing subpoenas, but it is hardly a "right" in the context of the constitution. However, that is just rhetorical hairsplitting and is probably more of an emotional issue than a legal one, but they aren't winning PR points from it.
DePaul University says they just don't have the information to comply. Between dynamically assigned IP addresses and multiple users on a computer, it is difficult for them to tell who is using what IP address when.