Puzzle Pirates, frankly. Made by people who knew what they were doing, were extremely talented, independent, although eventually tried to hook onto Sega as publisher, almost killed the game and then re-purchased the game from Sega to continue as "re-indie" devs. Still going to this day with a stable player base of a few hundred. The game itself is very clearly hand-crafted and every one of the (few) developers left their mark on it. Feels completed and polished.

Outer Wilds is this game.

Cold Waters if you're hankering for some hot sub on sub action.

Surprised no-one pitched Elite:Dangerous. Certainly a labour of love to begin with, incredibly talented sound design, first space sim to VR, truly devoted to the original material... Still going pretty strong (had a few weak years) with updates (only 2 DLC-ish major updates of which were paid) a decade later...

Lost Odyssey. I haven't played Clair Obscur yet, so I one know how it compares, but for me Lost Odyssey is the pinnacle of turn based RPGs.

The Stick of Truth, obviously.

Semi-jokes aside, I am a bit sad that not a single person mentioned the first four Silent Hill games. The sheer influence that series had on video games as a whole, especially in the horror genre cannot be overstated. But I guess it is tricky with games because everyone has different tastes and interests. It is rare that games unite people the way lord of the rings did. Gaming is at once so broad and so niche.

Zelda OoT, Majora's mask, BotW, TotK

No one mentions Red dead redemption. This world doesn't have any change.

Baldur's Gate 3

As far as labors of love go, Stardew Valley is probably the most current example. People paid for this thing years ago, but Concerned Ape keeps adding new features anyway. The retro graphics give this thing a timeless quality out of the box, so it already looks "dated" - this hasn't stopped the robust player community around it. We'll probably see this game stay relevant for a long time.

Dwarf Fortress.

Half-life.

☼Dwarf Fortress☼

Baldurs Gate 3.

Terraria

Java modded Minecraft.

Morrowind

One Shot
Outer Wilds
Portal

Chrono trigger