Patient Gamers

Does Don't Starve fit your bill?

Also second Submautica.

I feel like Valheim fits this to a certain degree

World of Warcraft Classic. You start as a no one. Everybody around you seems to know what to do. Your items are shit. You look like a peasant. The silliest enemies force you to rest and are able to kill you.

It‘s challenging but so rewarding. It makes you feel grateful for every single lvlup, item and skill you can get.

Even after spending literal days of your life, there always will be people who are better than you. Everything is said and done. Still this game manages to pull me back in from time to time. It’s so much fun.

Everything by David OReilly

probably rain world you are the protag in that game, but you're also just one part in this huge procedurally simulated ecosystem not to mention, the game is really hard

Outward is really good for this. You aren't the chosen one, you aren't special, you're just a person trying to get by and the game really makes sure you know it haha

Elite:Dangerous star map size is staggering, it is roughly the size of our galaxy, after you make acquaintance with such scale if it happens that you look out of the night sky IRL and see some nice stars think again, for some of the celestial bodies you see and think they are stars might be instead, for many are indeed, other galaxies entirely, as big as our or even larger, but so far out in the universe that we can perceive their light from here just as a pin of light.

Also read here: https://hitchhikers.fandom.com/wiki/Total_Perspective_Vortex

Fear and hunger.

It has enemies that are tougher than they should be. You are just a small part of the story. It's pretty good.

Everspace 2

The scale of the in-game universe is quite vast. Beautiful game too.

There was a Tom and Jerry game for super Nintendo. Granted I was 7 and sick, but that Bitch made me cry.

NaissanceE is really good at providing this feeling in the Eldritch sense, I don't know if it's up your alley as it's a pretty linear game about walking through a mega structure that looks like the eastern bloc itself went on an acid trip, but I came away with my time from it feeling like an ant on the sidewalk

the last federation? dark souls? X4? Dwarf Fortress?

Lots of survival games have a feeling like this.

This War of Mine State of Decay Ark: Survival Evolved but that is something you need to spend 100’s of hours in Mount and Blade: Warbands/Bannerlord

Wandersong. The whole plot is about the protagonist being a nobody and having no chances to change anything. It's not an action game or anything but I loved it, it was beautiful.

Some might disagree with me but I feel like The Last of Us falls under this, it's also just an excellent game with an excellent story.

One word Pathologic

I haven't seen:

Night in the Woods

Or

Don't Starve

Mentioned. Idk if they fit the bill, but came to mind.

Thief The Dark Project.

Pokémon: Legends of Arceus. Those alpha Pokémon will fuck you up

kinda a weird game but it definitely fits your request : everything

ETA: This review from polygon explains it well!

Haven't played, but I've heard Tyranny has this feel. Though it's a very different style of game, and you're essentially playing as the bad guy instead of the hero.

Or there's always the Dark Souls games, where you have to claw your way through each encounter.