First things first. The Geneva Convention DOES apply. Period.
Even the White House has admitted as such.
The point of contest would be whether or not they qualify as POW's, which would signify WHAT PORTION of the "Geneva Convention" would apply to these "combatants".

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While the Third Geneva Convention details the protections to which POWs are entitled, the Fourth Geneva Convention (GCIV) stipulates different protections for "civilian persons in a time of war," as Media Matters for America has repeatedly noted. The International Committee for the Red Cross (ICRC) -- the organization that pioneered the concept of international humanitarian law and has monitored compliance with the Geneva Conventions for more than 140 years -- has argued that the so-called "unlawful enemy combatants" currently detained at Guantánamo Bay are entitled to protections under GCIV. Its 2003 legal analysis titled "The legal situation of 'unlawful/unprivileged combatants" concluded that "unlawful combatants" are entitled to "the right to 'humane treatment' as defined in Articles 27 and 37 [of GCIV], and thus the prohibition of torture and ill-treatment; as well as the fair trial rights contained in Articles 71-76 [of GCIV]."

Indeed, even the Bush administration has acknowledged that detainees who are not POWs may still deserve other protections under the Geneva Conventions, though it has not specifically invoked GCIV. Contrary to Time's suggestion, the administration has distinguished between Al Qaeda and Taliban detainees with respect to the conventions. On May 7, 2003, the White House announced that the conventions do apply to suspected Taliban detainees, but not suspected Al Qaeda:

President Bush today has decided that the Geneva Convention will apply to the Taliban detainees, but not to the al Qaeda international terrorists. Afghanistan is a party to the Geneva Convention. Although the United States does not recognize the Taliban as a legitimate Afghani government, the President determined that the Taliban members are covered under the treaty because Afghanistan is a party to the Convention.

In debating the classification of the Guantánamo detainees, the ICRC has repeatedly cited its 1958 analysis of GCIV, which asserted that under international law, all detainees are either POWs, civilians, or medical personnel -- regardless of whether a particular leader or country chooses to apply a particular term to them:

Every person in enemy hands must have some status under international law: he is either a prisoner of war and, as such, covered by the Third Convention, a civilian covered by the Fourth Convention, [or] a member of the medical personnel of the armed forces who is covered by the First Convention. There is no intermediate status; nobody in enemy hands can fall outside the law. (Commentary: IV Geneva Convention Relative to the Protection of Civilian Persons in Time of War, Geneva, 195
http://mediamatters.org/items/200506060005