Baldur's Gate 3 is the modern king of that. Early example for instance, a boy steals a man's locket. The man is obviously upset about that and you can intervene and either side with the man or the boy.
Or while everyone is distracted you sneak up behind the boy and steal the locket from him. And when you then convince him to give it back he's amazed that someone managed to rob him.
Then you can give it back to the man and steal it again and hear him commenting about that.
TDTTOE goes way back! I first heard the phrase when I discovered Nethack. My favorite example from that game is when you try to dip a potion into itself you get: "This is a potion bottle, not a Klein bottle!"
It's kind of a spoiler for a spoiler-averse game but Void Stranger has some.
Void Stranger
The game autosaves only between rooms. Quitting the game lets you reset the room without losing a life, and it's a turn-based puzzle game, so you got time for it. But if you repeatedly cheat that way, you find out the developers were keeping track of ways you can abuse this, and you will get punished appropriately.
The granddaddy of them all:
NetHack
Outer Wilds base game spoilers
You know the gravity cannon on Ember Twin? When I was watching someone's playthrough, a weird question came to my mind: why here? Why is the cannon was put on Ember Twin, of all planets.
Amusingly, there IS a reason! The planet is filling with sand and, a few minutes before supernova, the cannon becomes completely inaccessible. Incidentally, a few minutes before supernova, the Interloper gets consumed by the expanding sun.
The placement of that cannon is anything but accidental.
Hades seems to have (multiple) voice lines for literally every situation. Idk how they managed to fit all that voice acting without making the game ridiculously large, but I'm still finding new dialog thousands of hours in.
The Pokémon games have a lot of these. One in particular is that in Generations 3 and 4 they added a mechanic to prevent the player from stranding themself by releasing the last Pokémon they have with certain HM moves.
For example, say your obnoxious younger sibling is mad at you. They "borrow" your game, use Fly to go to the obligatory island town, release all your Pokémon except for the weakest one, sell all your item, and waste the money by repeatedly buying and selling items until you don't have enough to buy anything useful. In Generations 1 and 2 your only real way to get out of this scenario is to trade your remaining Pokémon with one from another cartridge that has either the move Surf or Fly. In Generations 3 and 4 the last Pokémon that knows an essential HM move will refuse to be released. Generations 5 and 6 don't have this feature because there aren't any islands. From 7 onwards the HM system was replaced entirely.
Red Dead Redemption 2 has a level of detail that surpasses any other game I can think of. The birds alone are hyper realistic for no clear reason.
If you disturb birds they will fly away and if you follow and watch them they form flocks the same way/shape the exact species does IRL.
Plus many of the other mechanics in the game like the horse physics are unnecessarily realistic IMO, but hot damn if it isn't incredible.
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