Rimworld for me.
(I have never tried Dwarf Fortress.)
Honorable mention goes to War Thunder, while it isn't on of my favorites, I was still a bit blown away to find out it runs natively on Linux.
I'm not sure if I have a favorite game but if I had to choose one I'll probably have to say Dungeon Crawl Stone Soup given the amount of time I have spent with that game.
Borderlands 2. Give me a mindless Diablo With Guns experience any day.
I didn't know there was Linux port of this game, nice!
There was a native release from the jump, it was always kind of jarring being able to install it without selecting a Proton version first.
Nice! Shame that Borderlands 3 does not have it and you need to run it through Proton. :c
A great game I haven't seen mentioned yet is The Talos Principle (1) that also has a really good native port using Croteams Serious Engine.
I'm gonna say Valheim, even though the native version doesn't respect your default audio device so it can end up outputting sound to the wrong device at startup, which you can then correct using a volume mixer.
That's the reason why I still play the Windows version via Proton though.
But you were asking for my favorite game with a native Linux port, not for the game with the best Linux port :D
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Most of mine have already been mentioned; KSP, Rimworld, Stellaris.
So I'll add one of my all time favourite games and say XCom and XCOM 2. I've sunk hundreds of hours into xcom 2 with various mods.
Close second is Crusader Kings 2, and close third after that is Empire Total War.
And of course CIV. It's not a proper list without CIV.
I've been playing both Oxygen Not Included and Celeste regularly.
Tomb Raider 2013 reboot, although today the windows version under proton actually performs significantly better than the linux version
Team fortress 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
Gaming on the GNU/Linux operating system.
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