My favorite is in the Dawguard DLC for Skyrim. If you somehow get far enough into the DLC to enter the Soul Cairn and you didn’t do the main story quest where you kill your first dragon, you’ll get unique dialogue with a dragon you meet in the Soul Cairn. He calls you Dovahkiin, and you can ask him why he called you that, to which he responds something like “I do not know, it just felt right to call you Dovahkiin. Perhaps you will learn why soon”
Basically all of NetHack, but if I had to pick one thing, it would be the fact that the devs foresee things that don’t even exist in the game. For example, if you polymorph yourself into a monster that can eat metal and then eat a trident, you get a humorous message referencing Trident bubble gum. A similar message exists for when you eat a piece of flint (referencing the Flintstones, naturally), despite the fact that there are no monsters in the game that can eat rocks. In other words, that message can never be seen in the vanilla version of the game, but the devs prepared it anyway just in case you mod such a monster in.