Over at Balkinization, Jack Balkin has an excellent post on the Padilla indictment. An excerpt:

  By indicting Padilla now, The Bush Administration moots Padilla's appeal to the Supreme Court. It also leaves standing the Fourth Circuit's decision in the Padilla case, which broadly upheld the President's power to detain U.S. citizens like Padilla as unlawful combatants. . . .
  That result is particularly worthy of note, for the Fourth Circuit opinion may yet come in handy if the Administration needs to hold another U.S. citizen within the geographical boundaries of that circuit. The Administration now knows that the Fourth Circuit is a Constitution-free zone. It can, if it needs to, declare someone an enemy combantant, thrown them into a military prison, and interrogate them at its leisure. It will take years for a citizen to exhaust his appeals and reach the Supreme Court; and when the citizen finally gets to the Supreme Court, the Administration has the option to indict and moot the case (as it did with Padilla) or, if the Court's personnel have changed sufficiently in the interim, risk an appeal to the Supremes.
  You may recall that, following the Hamdi decision last year, the Administration decided not to give Yaser Hamdi a hearing, but instead released Hamdi to Saudi Arabia, extracting in return a surrender of Hamdi's U.S. Citizenship and a promise that he would not sue. Now it has indicted Padilla to avoid facing a simliar rebuff by the U.S. Supreme Court. In both cases, the Administration argued that that it was of the utmost necessity to detain them indefinitely and that it could not give these men the constitutional protections ordinarily afforded criminal defendants without severely damaging national security. These assertions now ring hollow-- Hamdi is free, and Padilla is in the criminal justice system.