I had a nose around on the web and found out this…
Apparently the USAF has 7 Boeing 747s. There are four E-4B airborne command posts which are "militarized versions" of the 200. Two more 200s are designated as "Presidential Aircraft".
The only 400 is being converted into an experimental YAL-1A "Attack Laser" which you might think sounds a bit far fetched. Apparently it's going to have a powerful laser mounted on a nose turret. A fleet of seven aircraft are planned to be operational by 2008 and they will form part of the anti ballistic missile system – supposedly able to “detect and destroy theatre ballistic missiles in the powered boost phase of flight immediately after missile launch.”
Whatever your feelings about the ABM programme (personally I think it’s an extremely dangerous direction to move in) it is rather worrying that a civilian airframe is going to be used to carry a critical component of the system. Will a “rogue state” interested in clearing the local skies of US ABM capable aircraft be able to tell the difference between a civilian 747 and a YAL-1A?