[AgentZero]

How about a 'Station Construction Kit' component? Basically, you equip a ship with this component, send it out into space somewhere, and when you activate it, it creates a space station. The station created would be one of your existing designs, and the component would have a very small construction rate, so it would only realistically be useable to set up small resupply bases.

Also, I think Bases built in 'empty' space should have to get their construction materials from somewhere. At first, it would only be possible to have Space Yards construct things if they're built in asteroid fields or around planets (colonized or not). Eventually you could research something like 'Mining Drones' which, when equipped on a Base would allow you to build the base anywhere you wanted. As for how to get the base there in the first place, see the above suggestion.