Does the government have to follow the Geneva conventions in dealing with Terrorist outfits?

This subject has been discussed at great length especially since terrorists attacked the United States (US) on 9/11/01. It was brought to light by the treatment of prisoners in CIA-run prisons and at places like Guantanamo Bay. In July, 2006, the US Supreme Court ruled that the Geneva Convention did indeed apply to terrorists because the US is a signatory to the Geneva Convention provisions that prohibit cruel and inhuman treatment of detainees.

However, many argue if the terrorists are from nations that have not signed the Geneva Convention, these terrorists should not be subject to protection under the Geneva Convention. If this issue has been resolved, I do not yet know.