Stanley Parable, the entire game is about making fun of the player.

Super Paper Mario's line "I love going on message boards and complaining about games I've never played." is really good.

Multiple games have done it, but something along the lines "try not dying" as the loading screen tip after dying about a dozen times is always funny to me.

In Pokémon Ruby/Sapphire/Emerald, the NPC who asks "where are you from" and we get the options "yes" and "no".

(He has not heard of yes town, nor does he believe we don't come from anywhere at all.)

I always talk to Hypnos in Hades when I die. he always talks shit about how you died and it makes me laugh.

I love the sass.

There is a spot in Space Quest 6 where you can skip a puzzle and go to the solution immediately... If you already know what to look for. I tried that once, since it was not my first run and I remembered the last step.

At first the narrator wonders how you did that, then he assumes you've been using a walkthrough. He shames you and punishes you by slowly draining your score counter... Before reverting it and telling you not to do it again.

There's that bit in Baldur's gate 2 where some NPCs decide they can take you on, die, and then reload the game.

My favorite will always be the 'Spent 15 Hours at the Alien Strip Club' achievement in High On Life.

In Postal 2 there's a platforming section and, because I suck at platformers, let alone in first person, so I was saving a lot. After a few very short and successive saves, the dude made fun of me for saving so much.

Also in Portal 2, just a lot of GlaDOS lines in general.

In the original Warcraft games (not World Of Warcraft), repeatedly clicking units would initiate irritation voice lines.

Humans would say something like, “why do you keep touching me?”

An elf said something like, “you never touch other elves like that!”

Portal and Portal 2 are packed with passive aggressive remarks. One of my favorites:

Well done. Here are the test results: You are a horrible person. I'm serious, that's what it says: "A horrible person." We weren't even testing for that. Don't let that horrible-person thing discourage you. It's just a data point. If it makes you feel any better, science has now validated your birth mother's decision to abandon you on a doorstep.

The "Plenty of Fish in the Sea" achievement.

In Shadow Complex, a shameless ripoff of Super Metroid in its game mechanics, you play a guy who drives a girl out to a remote location in the Pacific Northwest and she gets kidnapped by a military organisation. You're cut off from your vehicle, but fairly early on in the game you are able to return to the start point. You are able to get in the car and drive away and an achievement pops saying "Plenty of Fish in the Sea." So you win but your guy gives up on his girl, leaving her to her fate.

Hack/NetHack had a similar thing where you could just leave without completing the main objective (retrieve the Amulet of Yendor, which has a random chance of appearing at the 35th level and below, and make it back out with the Amulet). I remember it saying something snarky on the Amiga version, but I don't recall exactly what. Like it said you went on to live a boring life or something like that. Any time you felt like you were locked out of the objective or outnumbered by enemies without the means to fight through them, you could backtrack and leave (though, things like disease, hunger, and thirst could take you before you got out) and you'd "win" (as in, you get to keep living).

Quit messages in old shooters like Doom, Heretic, Quake, and Duke3d.

"Are you sure you wanna quit? Press N to continue kicking-ass and chewing gum. Press Y if you're a little pussy bitch."

In Wasteland 2 there is a museum of pre-war artifacts. One item is an undetonated nuclear bomb. If you monkey around with it you can find a big red button. It is obviously a terrible idea to push the button. If you still decide to push it you get a special game over screen.

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I enjoyed Wolfenstein 3D's quitting messages, "Chickening out already?" or "Press N for more carnage. Press Y to be a weenie." and the like.

I would have swore there was a moment in Disco Elysium where a character makes fun of you for talking like you are trying to exhaust all the options in a dialog tree. But now I can’t find it. Anyone know?

Risk of Rain 2's death messages crack me up.

That was definitely not your fault

That was absolutely your fault

Come back soon!

ur dead lol get rekt

And so on

In Sam & Max Hit the Road, when you repeatedly try to pick a stationary object up. https://www.youtube.com/shorts/szTtHNEg6vo

This isn't quite in line with your question but it's adjacently meta:
the first time you fall to your death in Bastion the (amazing) narrator says "...and then he fell to his death. ... Ahh, I'm just foolin'." and then you respawn on the platform because videogame.

Crosscode has a ton of dialogue changed if you turn on NG+ modifiers, such as carrying over levels or using a "cheat code" for ludicrous damage, 1shotting almost everything.

One NPC quotes the "you cheated not the game, but yourself" copypasta.

The old point-n-click flash game Johnny Rocketfingers had a bunch. There was a part where you had to find a way out of a jail cell or something, and if you used the hand tool on a crack in the wall, your character just says "feels cracktacular."

Oh, and there was the old original You Don't Know Jack game where if you told the host "fuck you" or something similar in the answer box, they'd just lose patience with you and exit the game for you.

In one of the Leisure Suit Larry games, you get called out for saving the game too often during a particularly difficult section.

Having to grovel to lower the difficulty in God Hand.

Marathon (1994) has several call outs to the player when the AI giving you mission briefing calls the PC out for not caring and just wanting to shoot things. There's a lot of meta commentary in that series.