In terms of their implications for existing U.S. and international human rights and humanitarian law, the Bush administration's activities have been most significant in the detention, treatment, and trial of detainees held in connection with the "war on terror"--a conflict the administration has defined as including military activities in Afghanistan and Iraq, as well as military and intelligence activities worldwide against Al Qaeda and those "associated" with Al Qaeda or related terrorist groups of global reach.
The United States currently detains about 15,000 people in operations it considers related to the "war on terror," from Iraq, to Afghanistan, to a Navy brig in Charleston, South Carolina, to the U.S. naval base at Guantanamo Bay. (There are also reports of some dozens held at secret CIA and other detention facilities under unclear legal authority; I will not address these cases here.)
In the continental United States, there remain two individuals who have been designated "enemy combatants" by the President: Jose Padilla (currently in civilian custody, but who remains, according to the White House, subject to military detention at the President's discretion) and Ali Saleh Kahlah Al Marri. The President relies on both the Authorization for the Use of Military Force (AUMF), passed by Congress in the wake of September 11, and his commander in chief power under the Constitution, as sources of authority for these detentions. In the President's view, his power as commander in chief authorizes him to seize and detain anyone in the world--including in the continental United States--whom the President identifies as "affiliated with al Qaeda." Further, according to administration briefs, Congress may not have power to limit this authority through statutes like the federal NonDetention Act (passed following the internment of Japanese-Americans during World War II and requiring an act of Congress to authorize the detention of any U.S. citizen). The most recent administration briefs in court cases challenging the President's authority in this realm do not mention the Geneva Conventions as a relevant limit on executive authority (or indeed invoke Geneva at all).
With respect to those still held at Guantanamo Bay, the President again relies on his authority as commander in chief to detain captives picked up in the course of armed conflict. Again here, the President points not to the traditional battlefield engagement between the United States and Afghanistan as the relevant armed conflict for the purpose of the application of the laws of war (and indeed, many of those now at Guantanamo were not captured in Afghanistan), but rather a "global" conflict against Al Qaeda, its affiliates, and other terrorist groups of global reach.
Finally, since the official handover of sovereignty from the United States to Afghanistan, and from the United States to the new government in Iraq, the United States no longer appears to rely directly on the Geneva Conventions (or on the President's authority as commander in chief) as the source of power to engage in ongoing detention operations in those countries. Rather, according to letters to the UN Security Council from the U.S. Secretary of State, the United States now holds detainees in Afghanistan under UN Security Council Resolution 1566, which generally states to take necessary steps to prevent the commission of terrorist acts. In Iraq, the United States says it now holds only "security detainees" under the authority of UN Security Council Resolutions 1546 and 1637. As a letter by Secretary of State Colin Powell appended to SCR 1546 explains, the United States "remains committed at all times to act consistent with obligations under the law of armed conflict, including the Geneva...