Subnautica has some creepy overtones.

I’d recommend Control by Remedy. It’s got some SCP vibe and has liminal spaces, spooky supernatural shit and great looking environments and game play.

Outer Wilds. It's better to play it without knowing much beforehand. All I'm gonna say is: it will make you feel very lonely and even vulnerable at times, although it's not a horror game by any means. It's a beautiful videogame with a mind-blowing story.

Half Life/Black Mesa. I replayed it recently and I had forgotten the level of unease that pervades most of it. While short of horror, there's been an obvious disaster, people are panicking, and it's unclear to the PC what is going on for most of the game.

I'd say Arkane's Prey hits that for me. The feeling of isolation, not only on the station, but by virtue of being in space, and the story itself. The mechanics of the mimic enemies can create emergent jump scares, but I'd definitely say it's not a horror game.

I'd also say Death Stranding, at times. While the human NPCs are very wholesome, the atmosphere and experience of delivering the packages out through the timefallen wasteland and that isolation lends itself well to introspection and the BTs are pretty creepy and axiety-inducing until you're used to them and can fight them.

• Bloodborne

• Control (definitely what you're looking for)

• The Last of Us

• Little Nightmares (quite similar to Inside, horror-inspired and creepy but barely any jump scares)

• Inscryption

• Dying Light (admittedly not very scary, but at night where you get chased by creatures can be very intense)

Portal series

Control does a good job of starting out uncomfortable and weird, and continuing to escalate as the story progresses. A great deal of unease since you don't understand what's going on with your character or the environment she finds herself in.

Hellblade: Senua's Sacrifice kinda fits this description. It's a game about a mentally ill viking(ish) warrior so it's more "psychological" creepiness than zombies, but it definitely achieves what it seeks out to do as with its atmosphere without being outright horror. The game is not for everybody since the gameplay can be a bit offputting.

STALKER for that horror undercurrent, Deus Ex Mankind Divided probably has the best atmosphere of any game I've ever played and the fact the franchise was abandoned for that marvel brain-rot is a crying shame.

What Remains of Edith Finch. It's not horror at all but you're the last person alive in your family, exploring your childhood home, which is a crazy house with tons of weird add-ons and secret passages, exploring how your family members died. Mental illness, insane unlucky accidents, all that. It's a really truly excellent game. It's unsettling in a way that keeps you on edge without ever being actually afraid

I've been playing DREDGE and it definitely has the creepy element down. It's gotten me hooked for sure

Segments of most 3d Zeldas are like this, but the one that takes the cake is definitely Majora's Mask. The entire game is like one bad dream.

Most Metroid games also qualify, which makes sense since they draw heavily from the Alien movies.

Hollow Knight

Firewatch. The story and gameplay don't lead you to believe you're in for a paranoia existential plot but it certainly goes there. Sounds right up your alley. It's an amazing game and certainly hits the point of scaring you without jump scares with an uneasy tension.

S.T.A.L.K.E.R.

it's about scavenging and fighting in a radioactive exclusion zone in Ukraine

it has some monsters, that scare the shit out of me, and 'anomalies' that break the rules of physics

it's really good

Returnal. It has an unsettling atmosphere on an unknown alien planet and a mysterious story that you piece together. It’s very tense and you are isolated with just your character’s thoughts, I highly recommend it.

GMOD.

Something about Source engine maps set in realistic locations devoid of anything but a player has an overpowering creepy, liminal space vibe.

I'm surprised I haven't seen Morrowind in the comments yet. The storytelling gave me the impression that Todd Howard must've played a lot of DND campaigns while under the influence of psychedelics just to lay the setting for the plot. I highly recommend because I've had a lot of moments throughout my playthrough asking myself "wait, did that actually happen?" And, "Is this a Bethesda bug, or is the game straight up cursed?". Also, Many of the characters, creatures, and a certain "house", or faction in the game are straight up Lovecraftian, with aesthetics pretty on par with Bekzinski's art-style. I also think the Marathon series fits the bill on a lot of these aspects. It's Bungie's precursor to Halo, and while its narrative may be similar, I think the devs had to get creative with the limited software capabilities available at the time and so the narrative ended up being an experience I'd describe as "wild and uncanny".

Check out Manlybadasshero's channel, he plays a lot of games like that. CJU does as well. A lot of them are very narrative-based, which might not be what you're looking for. The Coffin of Andy and Leyley for example, freaking fantastic game but it's a slow creepy burn rather than action-oriented. Little Misfortune is another personal favorite, and the Tartarus Key. They also play some random ass games like this https://www.youtube.com/watch?v=2VWL4vKRp8U where it's a dystopian world and you never really find out what's going on, which sounds similar to what you're into.

There's 2 indie games that are SETI simulators. The original is Signal Simulator. It spawned a newer one, done like a half life clone, called Voices of the Void. Neither game is outright horror, but both give you a feeling of isolation induced paranoia. You feel like you're constantly being watched. There's a few random events that are creepy, but the idea is not outright terror.

I think Oxenfree has an eerie atmosphere. I haven’t played the second one yet since it got released just a few days ago, but I really enjoyed the first one.

Gone Home

Pathologic 2. Eastern European absurdist psychological "horror". Definitely what you are looking for.

Vampire the Masquerade, Bloodlines. Came out before HL2 and I still go back to it ever year or two

Outer Wilds. It isn't the whole game, but there are parts that will chill you to the bone.

Firewatch is a good example of this. Wandering round an empty forest, seeing an evergrowing forest fire all the time. It's quite eerie but not outright horror.

I never did finish it, but The Solus Project is, I'm pretty sure, exactly what you're asking for. 2017 first person exploration game, very environmental, set on a subtly creepy and somewhat confusing alien world. I got a copy in my Steam library...somehow that was cheap enough I don't remember and played a big chunk of it a couple years ago.

Less action than the Half Life/Unreal/Marathon alien horror FPS lineage, but similar feel.

I saw a game that fits this bill mentioned on two videos recently. It's called BABBDI and you explore a eery city where everyone you meet can't move other than to twist their heads to look at you. Nothing ever puts you in danger and that's established right away. But everything looks... Off.

Little Nightmares comes to mind.