If I read this right, even Justice Kennedy is ruling that the Geneva Conventions apply to the War on Terror:
The Court is correct to concentrate on one provision of the law of war that is applicable to our Nation's armed conflict with al Qaeda in Afghanistan and, as a result, to the use of a military commission to try Hamdan. That provision is Common Article 3 of the four Geneva Conventions of 1949.
The provision is part of a treaty the United States has ratified and thus accepted as binding law. By Act of Congress, moreover, violations of Common Article 3 are considered war crimes, punishable as federal offenses, when committed by or against United States nationals and military personnel. There should be no doubt, then, that Common Article 3 is part of the law of war as that term is used in 821.
This is a big, big deal. I cannot imagine, moreover, that Kennedy's reference to "war crimes" is casual here. Perhaps others read this differently, but this seems like Kennedy is firing a major shot across the bow of the Bush administration: Clean up your act on torture, because John Yoo and the rest of the crack legal team that carved out an exception for Al Qaeda detainees don't have a legal leg to stand on.