Panzer General is great on the surface but once you start to play it in depth you will notice it has ridiculous dicerolling.
Zero star green infantry can easily slaughter your 5 star elite shock troopers. :^(

The old X-Com games come to mind.

Oh I forgot: Team Fortress 2.

It really punishes you, you keep dying to sniper headshots by cheaters who never miss, and when you finally lose, the game starts ridiculing you with comments like

"ez"
"git gud"
"get rekt"
"cyka blyat"

and so on.

Recently, spending 20 minutes looting on PUBG only to be shot at by a suppressed AR/SR from who knows where and die near the end... Game is still addicting though so there's that.

From games that are meant to be hard and which aren't unintentionally broken, The Hitchhicker's Guide to the Galaxy game comes to mind.

Commandos 2 was ridiculously easy...no challenge at all, was just tedious.
The first game was pretty challenging (and fun), but it's all doable.

Meh, show off :P
Honestly it was for myself, first was nearly as bad.

Gradius 3, arcade version. I hate that thing.

Definitely NetHack. There is no comparison. It's practically impossible to beat this game without save scumming.

I remembered another:

The NES port of Might and Magic 1. While the game is mostly manageable, if a Locust Plague gets a chance to act, then it's game over. Due to a couple bugs in the game, the Locust Plague will hit for 255 damage (knocking out whoever gets targeted), which will trigger a bug which prevents the surviving party members from acting this round, allowing the Locust Plague to knock out another character. Repeat until entire party is dead. Do you think that's fair?

Fortunately, other versions (like the DOS version) don't have these bugs, and the Locust Plagues, to my understanding, only do like 10 damage total, making them manageable and fair.

Spelunky is difficult to win, sure, but I wouldn't say it's "punishing". Unless you're an advanced player tediously farming each level for cash to get some ridiculous score, a full playthrough takes well under an hour (meaning you'll have lost little, time-wise, with any given death). There are even shortcuts you can unlock that let you start in later areas of the game (though, counter-intuitively, you'll usually have a better chance of success when starting from the beginning, so the shortcuts are mostly good for practicing moving around, surviving, and experimenting in later areas of the game).
(Unlocking the final shortcut, though...that can be a bit punishing. ;D )

Also, most deaths, at least in hindsight, should be predictable. I'd say no more than 10-20% of deaths are "bullshit" deaths stemming from the procedural generation of the levels & placement of enemies screwing you; the rest will be player error -- whether that means failure to plan ahead, inattentiveness to your surroundings (e.g., because of rushing too much), pressing the wrong button (or the right button at the wrong time), or just generally going somewhere you should've avoided (excessive greed kills in this game).

While you are right in that the game is hard, it is hardly unbeatable. We (I myself and my friends) as a kids completed it on actual hardware (no savestates!). You just have to use all turtles (don't forget to swap!) and grind for pizzas and sub-weapons (especially "scrolls", which can kill that flying "astronauts" you are referring). Failing that, you can use cheap tactics (which helped us to beat the game in the first place!): use Donatello, hit an "astraonaut" just as it appears (on the extent of the weapon's reach) and stop immediatly! The "astronaut" will recoil after taking hit and slide trough the screen to the right. Guess what? It will not return (the same engine bug as in Ninja Gaiden and many other Famicom games with disappearing enemies if they leave the screen)! Bom! That awful hallway just have become easy as a piece of cake!
If only there was a way to get to the Technodrome without trial and error…

Civilization V when you play against BranjoHello, with opponent's commitment to win set to anything above 75%. :D