There were several. A couple of examples: the shuttle could delay release of a payload, maneuver while in orbit, release the payload, then maneuver again. So conceptually, you just put a satellite into an orbit and your enemy doesn't know exactly what orbit its in. I'm sure eventually they would find it, but the military still wants stuff like that.
Another example is the ability to grab a satellite and bring it back to Earth. To my knowledge, this was only ever used with the "long-duration exposure facility" because it'd probably be considered an act of war to steal another country's satellites but here again, it's the kind of thing the military would ask for.
So the idea is that the shuttle launches with a secret payload, and every 90 minutes you see it pass overhead. This goes on for days or weeks. Eventually it lands.
What happened? Well what you don't know is that on day 2, while it was over the Pacific and you weren't tracking it, it fired the OMS, deployed a payload, then fired the OMS again to return to it's previous orbit.
There's a whole other satellite out there and you don't know about it until you find it by some other means. And eventually you will find it. But the military is happy to pay for that short window of subterfuge.
[1] https://en.wikipedia.org/wiki/Boeing_X-37
[2] https://www.thedrive.com/the-war-zone/36440/this-is-our-firs...
[3] http://www.spacesafetymagazine.com/aerospace-engineering/spa...
According to wikipedia those things cost around $6 million to manufacture and spacex was the first to ever bother retrieving them.
HEXAGON KH-9