In Disco Elysium the game straight up called me out for apologising so much. It hit me so hard I stopped apologising as much irl. 10/10 game would be ashamed again.

Far Cry Blood Dragon's tutorial section. The game is very aware of how impatient gamers are to get to the killing, and milks it for all the time it can while the PC grumbles about annoying tutorial sections. They throw in a ton of extra dialog boxes like accompanying reading recommendations, obvious tips,etc.

The whole game is meta and corny on purpose. If you like '80s action movies and sci-fi, they packed just about every trope possible into this thing. Heavily recommend if you haven't played it.

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.

Eternal Darkness on the GameCube

It makes the Volume go up and down and a bunch of other wacky things.

Frets on fire tutorial

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."

Baba is you

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.

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!”

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

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.

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

Outer wilds, if you manage to

Like, “well done dipshit, I guess this is the end”.

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.

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

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.

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

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

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?

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

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 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.

Really love the moonman talking to you on every boot up. I always find myself looking forward to seeing what he says.

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.)

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.