Kenshi

Caves of Qud

Entropy Zero / Entropy Zero 2

MINERVA

Squad

Road to Vostok

Citizen Sleeper / Citizen Sleeper 2

Risk of Rain / Risk of Rain 2

Terra Invicta

Ghost Song

Sifu

... and if you have an inkling toward the OG 'walking simulator'...

Dear Esther: Landmark Edition

I am mostly confident that all of those are either self published or published via what was at least at the time of original release of the game, a fairly small indie publisher.

EZ and EZ2 are technically mods for HL2 but they are pretty darn good and then quite good, respectively.

Dear Esther and MINERVA are also HL2 mods.

Squad is basically the old Project Reality mod for Battlefield 2, but made in Unreal Engine by at least originally about 75% of the old PR mod team.

Anyway, I tried to pick some games that are indie, but are not as well known, largely due to not being cutesy.

EDIT

Forgot this one:

If you want a tank combat simulator game, on approximately the same level of fidelity of a flight simulator:

GHPC / Gunner, Heat, PC!

For when you finally get tired of Warthunder/Gaijin's bullshit, lol.

I guess technically you could describe the ARMA games as 'indie' in that they are self published, but they're also fucking huge, and ARMA is basically the consumer grade version of the military simulators they literally sell/lease to real world militaries.

Also, I would say Disco Elysium, but at this point, you should pirate it, after all the bullshit the publisher has done.

(which is arguably the more cannonically accurate way to play the game, if you haven't yet)