One of my all-time favorites, and to me, the best game of the Wing Commander series, is Wing Commander: Privateer. Unlike the other games of the WC series, in this one you play a free pilot with your own inherited ship. At that point, you are completely free to do what you want. Fly around and hunt pirates, trade goods between worlds, do a little pirating yourself, whatever. There are mission computers in each base that give you randomized one-off missions, and there IS a plot to follow, when you feel like it.
Privateer was one of the first (if not THE first, since it was 1993) games I played that was open like that. It was months before I actually found the guy that started the plot – my memory is they only sort of mentioned him at the tail end of the manual (“talk to Sandoval, in New Detroit”) and once in a while the bartenders mention him too. I just enjoyed visiting the various ports, upgrading my ship and weapons, trading goods, fighting pirates the whole nine yards.
The game runs well for me via DosBox (though your mileage may vary), but there are some other options to play in Windows if you don’t want to tangle with that. Privateer: Gemini Gold is a remake using the Vegastrike Open-source flightsim engine. I have downloaded but not played that yet, but if there’s interest I can do up a review of that as well. Nice thing there is you can play Privateer on Windows, Mac and Linux.
I know flightsim type games have never really regained the foothold they had back in the 90s, where X-Wing, Tie Fighter and the Wing Commander series were some of THE games to play, but if you have any nostalgia at all for that era, or just want to play a classic of the genre, try Privateer.