I'm giving an emphatic shout-out to Strike Commander. That game was truly ahead of its time in terms of flight simulators that also served as story-driven games. It made the arcade-y gameplay of WC (which I love) seem like child's play by comparison. You also had to manage money made from missions to service your fighters and their load-out ordinance. Graphically it was unreal at the time it was released (1993), and as a kid visiting my best friend who had the only computer that could run it (486 DX/50) it truly blew our collective minds, as only old Origin "We Create Worlds" did during that time, ditto with Ultima VII and WC.
It also had a pretty complex geo-political setting and backdrop, especially for a kid playing it who was just starting to understand politics on a grander scale. It wove a prospective future from the old cloth & trends circa late 80s/early 90s, Middle East conflict, post-Soviet Russia, economic depressions, escalating terrorism that is pretty sophisticated for a game (and still pretty timely today). Actually, Strike Commander is set in 2011...so the future has finally caught up to it. That certainly seemed eons ago as a Junior High student!
Hell, some enterprising soul even transcribed the whole think onto wiki, so you can read it here:
http://en.wikipedia.org/wiki/Strike_Commander This is one release (if Dungeon Keeper and Privateer are any indication) that I'm take-it-or-leave-it in regards to the speech pack. I find voice acting in video games pre-1996 to be pretty camp. The use of professional voice actors hadn't yet caught on en masse. The Tactical Operations add-on would be nice, though not strictly necessary either.
Also, if Wing Commander does land on GOG, try to get the "Kilrathi Saga," which includes the first three games, and more importantly, configured to run on Windows. By the way, the out-of-print Kilrathi Saga is perhaps the most expensive second-hand game I've ever seen sold...truly exorbitant, so licensing it here on GOG for cheap digital distribution would be a real boon.