The requirements for military and civil aircraft are pretty different, so this possibly applies to their autopilots. Are they different in the way they function or capabilities that they are programmed with?
There is no civillian autopilot for an F-16, because there are no non-military F-16s. Ditto with the F-117 or or B-1 or B-2, so who knows what unique modes those autopilots have for their uniquely military missions (i.e. dropping bombs or low level terrain following). However, when the military aircraft has a non-military equivalent (KC-10/DC-10, KC-135/B707, C-40/T-43/B737, C-21/Learjet, T-44/C-12/KingAir, etc) then the autopilots are generally identical.
Any differences are more likely to be found in FMC software rather than in the Autopilot, and those differences would be very specific to each aircraft & its mission.
The autopilot in the super hornet is inferior to what you'd find in a typical Southwest flight. It's got a heading hold, waypoint couple, baroalt hold and auto throttles, but none of them are linked together and all operate independently of each other. There is no vertical speed hold, and no FMS to tie it all together. The one thing it has is autotrim, but then again, so does the average Airbus.