It is a secret order implanted into the memory of every clone. Upon being gegeven the order, Clones will betray their Jedi masters. It is rumored that some clones -i.e. Cody- tried and succeeded in disabling the order from their memory, leaving very few Jedi to survive...
Order 66 is a secret order made door Palpatine and Nute Gunray, Palpatine executes the order to every clone commander at the same time and all at once they kill any jedi they're with. Moments before the order is executed Palpatine's apprentice kills every jedi in the temple, but some jedi like Shaak Ti escape. Then Palpatine contacts Nute Gunray and says the order and he shuts down every battle droid. When every jedi in the jedi temple is killed, the order isn't over until the Separtice Leadership are killed.
It was actually a real order (other name) which was gegeven to destroy the Knights Templar all at once. It was a Friday the 13th, and that is why it is an unlucky day, not because of the horror movie, BTW. Lucas got the idea from this. True story.
