RealWeaponX: Wing Commander III, and TIE Fighter. Unfortunately TIE Fighter isn't on GOG. Freespace is one of the best, though. If you like RTS, try Haegemonia, or MOO. I suck at RTS, but I can't help loving them - sending hordes of tiny ships to their certain doom...
MOO 1 & 2 (aka the real ones) aren't RTS. The whole thing is turn-based.
Best Freespace-style experience is the Wing Commander series. X-Wing series is just as great in different ways, also very difficult in places. Iwar is the best real-physics combat series. Tachyon has some flaws but is very fun and pretty. X is the most successful freeform trading and combat series. You could also track down an old SSI game called Renegade: Battle for Jacob's Star. It used SVGA polygons, so it's not nearly as dated as it could be. It's closer to X-Wing than Freespace in feel. Archimedean Dynasty and Aquanox are WC style combat in submarines. There's one other old WC style game called Star Crusader that I was never able to get into.
MOO is hands down the best 4X series. Sword of the Stars felt closest to classic MOO to me with real-time combat added (avoid sequel, they're still adding basic functions a month after it was released). GalCiv is a lot like classic Civilization in space, with good AI and moral decisions to make. Space Empires series is kind of sterile, but lots of complexity. Also includes Star Fury, where you move a single ship around a 2D fake-3D map for combat and other missions. Imperium Galactica series and Haegemonia are flawed real-time 4X with unique strengths in atmosphere and storytelling. Homeworld and Nexus are great 3D real-time fleet management games. ORB and Star Wolves aren't bad. For 4X, Star Wars: Rebellion is very flawed and dated, Empire at War less so. Starcraft and Dawn of War if you want land-based space themed RTS combat. Also Star Wars Galactic Battlegrounds, which is reskinned Age of Empires.
There were some Star Trek RTS and 4X games but they weren't particularly good. But Bridge Commander and Starfleet Command are true classics.
Check out Strange Adventures in Infinite Space, Weird Worlds, Starscape, Ur-Quan Masters (Star Control), Space Rangers, and EV Nova for unusual 2D hybrids.
AI War is unique. It's a mix of tower defense and RTS attacking, with overall strategy based on taking only what you absolutely need. Every victory beefs up the opponent's tech level and resources. You'll like or hate it on its own merits. Knowing how to play other 4X won't take you very far.