I came upon this excerpt in Republic Commando: True Colors when i finished the book this weekend. It puts alot of things in context for people who have questions about Order 66.
Order 65: In the event if either (i) a mahority in the Senate declaring the Supreme Commander (Chancellor) to br unfit to issue orders, or (ii) the Security Council declaring him to be unfit to issue orders, and an authenticated order being received by the GAR, commanders shall be authorized to detain the Supreme Commander, with lethal force if neccessary, and command of the GAR shall fall to the acting Chancellor until a successr is appointed or alternative authority identified as outlined in Section 6 (iv),
Orde 66: In the event of Jedi officers actibg against the interest of the Republic, and after receiving specifcc orders verifed as coming directly from the Supreme Commander (Chancellor), GAR commanders will remove those officers by lethal force, and command of the GAR will revert to the Supreme Commander (Chancellor) until a new command structure is established.
-From Contingency Orders for the Grand Army of the Republic: Order Initiation, Orders 1 Through 150, GAR document CO(CL) 56-95
Basically, the Grand Army of the Republic (the clone army), had standing orders to kill or arrest anyone in power who betrayed the Republic. This is the thing that really makes me lose a bit of respect for the jedi, because they really got caught with their pants down. Not only should Mace have taken a cell phone with a camera in to arrest the Chancellor, but he apparently should have taken some clone troopers as opposed to jedi knights. The troopers could have at least verified the arrest once the jedi could prove that Palpatine had orchestrated the war.
That's pretty sloppy work for the detective jedi...
It is nice to know though that Order 65 also existed, and the 66 wasn't some implanted clone suggestion. I always thought that was a poor way to move a plot line, since that's how it came off in the movie, but after reading the Republic Commando series, you get a much better view into the training of the clones. From the time they were grown to the when they went to battle, all they did was eat, sleep, and train for combat, so it makes sense that their primary reading material would be contingency orders, weapons manuals, etc.