They still do.
The first order grants the president (and other officials, including the secretary of defense, the secretary of homeland security and presumably certain postal clerks) the right to declare anyone -- including an American citizen -- an "unlawful enemy combatant." A person so declared has no redress, no way to appeal, no ability to challenge that designation. Once a person has been named an enemy combatant, according to the Bush Administration -- and now to the Obama Administration -- he has no rights. He can be held without charges forever, tortured, you name it -- well, actually, the president or the secretary of defense names it.
In the second covert executive order, Bush authorized the CIA to target and assassinate said "enemy combatants" -- again, including American citizens.