Space Station 14, seriously one of the best games I've played.
Interesting that it hasn't come out yet. Did you play demo / playtest or what? I'm glad to see the Linux version.
There is a flatpak. It hasn't technically come out, however there are thousands of players right now. Though most are in russia. I would also recommended looking at the git repository to see how it's going.
My favorite native game is flight simulation X-plane since version 8. For kids Super Tux Kart.
X-plain seems fantastic for hobbyists and enthusiasts! Good to see a Linux port.
Realism You Can Feel
Everything in X-Plane operates from real world physics. Aircraft handling, ground effect, wind gusts, and more will give you the most accurate flight sim experience possible. Try it today!
Detailed World and Atmosphere
As you explore the X-Plane world, the weather, water, light, 3-D forests, and everything around you add to the immersion.
Analyze and Refine Your Flying
There’s no end to the customization you can make to your flight simulator experience. Adjust your approach scenarios, get real-time feedback, and use tools like X-Plane’s replays to study and improve your skills and confidence over time.
Yeah, that's the classic one. It would be weird if there wasn't a Linux port for something "Tux" related.
Flightgear is a 🄯Copyleft, GNU General Public License(GPL) V2, Open-source and Freely Modifiable flight simulator that champions principles of user empowerment, community-driven development, and unrestricted customization. It embodies transparency, inclusivity, and the spirit of collaborative innovation in flight simulation.
Dota 2
Since people have already mentioned Factorio, Dead cells, and Stellaris (which btw all of paradox grand strategy games since CK2 have native versions). I'll mention a lesser known game that me and my wife love to play, it's similar to Overcooked (which btw Overcooked 2 has native Linux support) but a lot more calm: Out of Space
Heroes of Might and Magic II, using the fheroes2 recreation engine.
My top answers are of course Kerbal Space Program, Dwarf Fortress and Stellaris.
However, all those have been mentioned already, so, to add something new to the list: Pathfinder: Kingmaker. It is currently my favourite cRPG.
Edit: Since you mentioned "Great Linux ports": Kingmaker has a game-breaking bug in the Linux version regarding Gamepad input. However, as long as you play it with mouse and keyboard (as the gods intended - insert PC Master Race meme), the Linux version is working perfectly fine. However, if you plan on playing it on the Steam Deck, you might want to play the Windows build.
The new Valheim update was pretty fun. I also like playing CS2
Open source, more modern, Ultima Online client. Still need the original art files. https://github.com/ClassicUO/ClassicUO
One of them would have to be Life is Strange 1, it's a pretty good port and honestly it's one of my fav games of all time.
I completed it on Windows before I knew what Linux was. I didn't know there was a native Linux port, thanks!