An excellent article by Jane Mayer in The New Yorker, "The Trial," points to a terrific reason for trying Al Qaeda terrorists in the court system rather than military tribunals.
According to Kate Martin, the director of the Center for National Security Studies, in Washington, the military can’t simply grab suspects inside the U.S. and hold them without charge or a hearing. “It violates the Constitution, which extends to everyone inside the U.S.,” she said. “You can’t be seized without probable cause. You have the right to due process, and to a trial by a jury of your peers—which a military commission is not.”