How realistic of a physics model do you want? If you want actual Newtonian Physics, I would recommend Independence War I and/or II.
Although not available through GOG, I would also highly recommend
- Star Shatter: The Gathering Storm
- Babylon 5: I've found her
Both use newtonian physics, Star shatter has a dynamic campaign and B5 uses a story driven (non-dynamic) campaign.
If you're not interested in realistic physics, any of the Freespace and Wing Commander games are good, although I would strongly lean towards WC 2-5. Great stories, and the graphics were way ahead of their time.
I'd recommend Freespace series for a good start, both are really good and very well balanced, Also Wing Commander is good too, 3 and 4 are the best.
I was looking at wing commander. Is there any specific order i need to play the games in order for the plot to make sense? or can I just skip to 3 and 4?
Need? You don't need to play them in order. I would recommend you find a synopsis of the story to read, though, for the game's story line to make a bit more sense.
Honestly, I would just play them all in order, it's worth it, IMO.