Managing Nuclear Weapons Custody
... Beyond the safety issue of transporting nuclear weapons in the air, the most important implication of the Minot incident is the apparent break-down of nuclear command and control for the custody of the nuclear weapons. Pilots (or anyone else) are not supposed to just fly off with nuclear bombs, and base commanders are not supposed to tell them to do so unless so ordered by higher command. In the best of circumstances the system worked, and someone “upstairs” actually authorized the transport of nuclear cruise missiles on a B-52H bomber ...
The last time the Air Force is known to have flown nuclear weapons on a bomber was during the so-called Chrome Dome missions in the 1960s when the Air Force maintained a dozen bombers loaded with nuclear weapons in the air at any time. The program, formally known as the Airborne Alert Program, lasted between July 1961 and January 1968. The program ended abruptly on January 21, 1968, when a B-52 carrying four B28 thermonuclear bombs crashed on the ice off Thule Air Base in Greenland during an emergency landing. The accident followed another crash in Spain in 1966 and several other nuclear incidents.
Between 1968 and 1991, Air Force bombers continued to be loaded with nuclear weapons and stand alert at the end of runways on bases across the country, but flying them was not allowed due to safety concerns. The ground alert ended in September 1991 when the bombers were taken off nuclear alert as part of the first Bush administration’s Presidential Nuclear Initiative.
Although nuclear weapons are not flown on combat aircraft under normal circumstances, they are routinely flown on selected C-17 and C-130 transport aircraft, which as the Primary Nuclear Airlift Force (PNAF) are used to airlift Air Force nuclear warheads between operational bases and central service and storage facilities in the United States and in Europe ...
http://www.fas.org/blog/ssp/2007/09/flying_nuclear_bombs.php