Here are a couple known projects that never made it to fruition:
The Air Force toyed with a project for awhile in the early 60’s called Blue Gemini which was aimed at ultimately putting Air Force astronauts aboard a Manned Orbital Development System. That idea was abandoned to pursue one of a Manned Orbital Laboratory—also abandoned. Everything about the Blue Gemini project was meant to be internal within the Air Force, so the possibility was there for unannounced launches and missions. All that was scrapped by 1969. SkyLab was the civilian implementation of the general ideas.
http://history.nasa.gov/SP-4203/ch6-2.htm
A shuttle-like vehicle, the Boeing X-20-Dyna Soar was another Air Force program aimed at getting Air Force astronauts into space. A mock-up was built but that project was also canned just construction on real hardware began.
https://en.wikipedia.org/wiki/Boeing_X-20_Dyna-Soar
Those are two of them. An old man I once new worked with SAC all of his career, and hinted they had many more ideas floating around.
Biggest problem seems have been cost per pound of payload. At some point, having a large number of armed and manned platforms in space was not cost effective.