The Space Shuttle flew a total of 135 missions in its lifetime. Of these 135 missions, seven were classified Department of Defense missions whose purposes were never officially announced.*

• STS-51-C (15th mission, January 1985) deployed a Magnum satellite designed to intercept communications, mainly from the Soviet Union and China.
• STS-51-J (21st mission, October 1985) deployed two satellites that form part of the Defense Satellite Communications System that allows the military to communicate with units all across the globe.
• STS-27 (27th mission, December 1988) deployed the first Lacrosse radar imaging reconnaissance satellite. It is alleged (on Wikipedia) that one of the uses of the Lacrosse system would have been to provide real-time targetting data to the B-2 Spirit stealth bomber.
• STS-28 (30th mission, August 1989) deployed one of the satellites that forms part of the second generation of the Satellite Data System (SDS2) which relays data from low-orbit reconnaissance satellites.
• STS-33 (32nd mission, November 1989) deployed another Magnum satellite.
• STS-36 (34th mission, February 1990) deployed a MISTY photographic reconnaissance satellite and the PROWLER satellite. MISTY satellites are alleged to have both optical and radar stealth capabilities to make them difficult to track. The purpose of PROWLER is uncertain, but it is probably designed to inspect other satellites and intercept signals; it has been tracked from Earth approaching close to Russian communication satellites.
• STS-38 (37th mission, November 1990) deployed the second of the SDS2 satellites.

There was also one partially classified mission:

• STS-53 (52nd mission, December 1992) deployed the third SDS2 satellite along with a number of unclassified experiments.

The National Reconnaissance Office, one of the seventeen “elements” of the US Intelligence Community, actually influenced the design of the Space Shuttle, having its payload bay size increased so that it could accommodate the KH-9 HEXAGON spy satellite. In the end all of the KH-9 satellites were actually launched by third generation Titan rockets.

* Everything in this post should be heavily prefaced with “allegedly”.