The Hamdan decison is 185 pages long and I haven't read it all. But I think that it may be less signficant with respect to the trial of the GiTMO detainees than it may be on other issues. The case does not appear to hold that detainees are subject to all the rights to which criminal defendants are entitled, only that they are entitled to more rights than the military commissions actually established provide. Hamdan, for example, was excluded from his own trial.
But a majority of the Court seems to have ruled that certain provisions of the Geneva Convention, i.e., the "common" articles, do apply to the war against al Qaeda. The D.C. Circuit had held that these provisons only apply to wars between nations. As you can read here, this may have implications for the form of permitted interrogation.