Mohammed and the other defendants, Walid bin Attash, Ramzi Binalshibh, Ali Abdul Aziz Ali and Mustafa al Hawsawi, are charged with conspiring with al Qaeda, attacking civilians and civilian targets, murder in violation of the laws of war, destruction of property, hijacking and terrorism.

They said in a 2009 letter to the previous tribunal judge that they were "terrorists to the bone" who considered the accusations against them "badges of honor" that they carried with pride.
In the article, it says that the Secretary of Defense can decide on the method of execution. Damn, I wish I was the Secretary of Defense, because I have the perfect punishment..... Strap them down inside a remote-controlled pilotless aircraft, and fly the plane into the headquarters of al-Qaeda. Include a note that says "Dear al-Qaeda. You can have your terrorsists back".

Article is here.