Linux Gaming

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.

Borderlands 2. Give me a mindless Diablo With Guns experience any day.

Team fortress 2. The best game of all times, if not for the bots

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 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.

Quake 3 sourceports, my favorite is quake 3e

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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

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.

UT2004

Devil daggers at the moment

Team fortress 2

Heroes of Might and Magic II, using the fheroes2 recreation engine.

https://github.com/ihhub/fheroes2

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

Tomb Raider 2013 reboot, although today the windows version under proton actually performs significantly better than the linux version

I've been playing both Oxygen Not Included and Celeste regularly.

Dota 2

Rocket League. It has an outdated Linux port that still runs just fine, just no online play, then runs great in Proton, too.

So technically, it qualifies.