Nothing
that secret. At least the E-6B "Mercury" TACAMO (Navy flown, but on a joint USAF/Navy mission now to connect submarines, missile silos, and the cheerfully named "national command authority" in case the big ugly balloon ever goes up).
Photo of one here:
http://uscockpits.com/Special%20Miss...y%20TACAMO.jpg
I know these guys have also done some stints orbiting over SW Asia (Iraq by another name) with some extra gear on board, helping with commo challenges there.
I've always wondered if this cockpit conversion was a one-off exercise for Boeing or if they planned to offer it to other 707 operators.
--Nick