My home airport is joint use- the local civilian government has an agreement to lease daily flight slots and the land underneath the civilian commercial terminal from Eglin AFB. There have been one or two times over the years when there was stuff the civilian side wasn't allowed to see. The plane would be going down the mini Polderbaan that connects the civilian and military sides and just before the runway turnoff, the pilot would come on and say tower has informed him of a DoD request that they go window shades down while on the runway because of the presence of in-development aircraft.
Stuff I have missed but seen by people I know:
The space shuttle- Eglin was an alternate refueling stop when they had to bring it back from California on the back of a 747 and their usual Texas refueling point suddenly got The Weather
One of the earliest (and possibly the earliest) longer distance flights of the 787. Like many companies, Boeing rents out the McKinley Climatic Lab on base for cold weather testing and they were down with it in Florida (yes, you do go to Florida to get a nice constant -40C temperature) as part of getting the plane certified for commercial use.