Hey, what you call X-COM is actually an european game called UFO:Enemy Unknown that only in America was called X-COM:UFO Defense. Also the GOTY easily.
You missed out some pretty good games both in your list and your extension list:
Sid Meier's Colonization is a pretty good game, a good refinement of the basic Civilization blueprint with some added ideas. And while Civilization is done and iterated about a lot, I see not a lot like Colonization.
https://www.youtube.com/watch?v=jdccnDJy5uY
Then we have one of the best fighting games ever, One Must Fall:2097. From a company Epic Megagames, not some losers only called Epic. It had cool stuff after fight, like a news recap and your mechanic telling you, your robot got too much damage.
https://www.youtube.com/watch?v=6fGM1cvUQv8
We have the open world adventure game Robinson's Requiem, which used Voxel graphics and simulated oh so many systems. For instance you had not simply health points, no you could be sick with all sorts of illnesses and could overheat or be too cool. Some degree of simulation I only ever saw much later again in Project Zomboid.
https://www.youtube.com/watch?v=H-Q1TBTV3ho
Then we have my most liked Doom clone: Heretic. It improved on so many areas. Graphics: now levels looked like real environments. Music: it had some cool tricks like ambience sounds woven in. Gameplay: if I remember right it introduced usable items.
https://www.youtube.com/watch?v=0Xklmh0dz2I
And I have also to name Wacky Wheels. It is actually not that special, but it was the first Mario Kart clone I played, and Mario Kart like games are always cool. Also it some pretty cool items to hit other players with, like mirroring their image or reversing their controls.
https://www.youtube.com/watch?v=0vVIiKp6xMs
