The Supreme Court has ruled in three of the major civil-rights cases which have come out of the current not-war: Hamdi, Padilla, and Guantanamo Bay. In Hamdi the Court held that US citizens captured outside of the USA cannot be held indefinitely in a U.S. military jail without a chance to contest the detention. In Guantanamo Bay, The Court held that the non-citizens held by the USA also had a right to challenge their detention in US courts. In Padilla, the Court held that his case had been brought in the wrong jurisdiction, so Padilla (a US citizen apprehended within US borders) is still being held without any charges being filed.
So, could be better, but it's pretty good—even this Court turns out to believe that people can't be jailed without trial. Scalia, to my surprise, supported Hamdi, and Thomas supported the W. Bush administration in all three cases. Thomas is scary.
For lots more on this see Prof. Michael Froomkin's blog.