US officials have told the NY Times that nearly a dozen authorized secret operations have been conducted since 2004 in Syria, Pakistan and other countries. Former Defense Secretary Donald Rumsfeld signed the classified order and Bush approved it.
The recent Syrian operation that killed 8 civilians fell under this order. Another mission occurred in 2006, using Navy SEALs for a raid on a suspected terrorist compound on Pakistani tribal ground.
The raids are usually by special forces, with the CIA, in an Al-Qaida target hunt. Most missions, including the Syria and Pakistan missions, have to be approved by the President or the Defense Secretary.