I'm pretty far into the game and have access to most clusters (right now I'm stuck on the turret mission with Jack - I can never shoot all the Thul in time) but there are a few clusters with ? systems or greyed out systems - even though I've visited every system in the cluster and, if available, done the sidequest.
Do I return to a lot of these places later and unlock them?

Sometimes you don't get the system keys until you do a later mission in a different system, but there really aren't a lot of those. The way you describe it sounds like there are too many locked systems. Perhaps if you got a screenshot of the map and posted it, it might clear things up.

I'll get on that - does the game have a built in screenshot function, or should I just print-screen it?

The game uses the Print Screen button to produce screenshots that it will automatically save in My Documents\Ascaron Entertainment\Darkstar One.

All right:
http://i44.tinypic.com/e5k7yb.jpg
It's just Arrack and Oc'to space.

How about the two grey systems on Arrack space, in the top left two clusters?

IIRC, those are also opened up by the story missions eventually.

Thanks. Now I'll get to work on trying to beat this horrible flak mission.