The kind of game you are talking about sounds a lot more like Elite than cRPGs such as those listed here. Seeing as a fair number of those have already been listed (Rogue Galaxy bears special mention, as it fits almost exactly the criteria by that interpretation), I'll list the ones I think of by my interpretation of what you say. The key thing I'm reading is "shooting up spacecraft", which I don't think is part of many games listed here so far.

Freelancer is middle-aged, but it's quite a bit of fun and fairly solid. That said, it isn't particularly deep, I found. Worth picking up for some good action, not for the more long-term build a personal fortune kind of stuff.

X2 and X3 are far deeper affairs. They've got a fairly large universe and what is ultimately a free-form setup, although there are storylines in each you can engage in. If you do ignore them, you have a very great deal to engage in anyway, trading, missions, alien incursions, even setting up factories and production lines and such.

I've never played Darkstar One, but it is apparently Elite-style, and from what I see has generally favorable reviews.

Other than that, you start getting into far more constricted things where you have a main mission you are railroaded along, but which allow side missions to be done. Although it's a PSX game, a good example of this is Colony Wars: Red Sun. Upsetting to those of us who wanted more Navy vs. League action, it was still a pretty solid and fun game that can suck up time.

And finally, if you want to get really hardcore, you play EVE Online. It's by far the biggest game world I've ever seen, with hundreds of systems, thousands of planets and moons, thousands of stations from which to get missions, and a vast, intricate economy which could require real-life knowledge of economics to fully exploit. Very, very time consuming, pretty darned hardcore if you want to get far in it, and very good if it's your bag.