The Obama administration recently announced that it would try Khalid Shaikh Mohammmed (and four others) in federal court for plotting the 911 attacks. I think this is a mistake. In my view there is no reason to grant these people the legal protections we give American citizens accused of ordinary crimes.
I see this as a political decision and would have Obama personally ultimately decide the fate of these prisoners. If he doesn't want all the responsibility let Congress ratify his decisions. Of course this is unlikely as politicians hate taking responsibility and routinely let the courts take the heat. But in my view this is no more the proper domain of the civilian courts than was the decision to bomb Hiroshima and Nagasaki.