Eh, maybe it's just me, but again, I wouldn't say it's any more punishing, just straight-up more difficult. Killing Yama might technically be tougher than carrying the key from the Mines all the way through the Ice Caves, but I'll be damned if the latter task doesn't seem crueler and more punishing to me than the convoluted process of entering Hell -- or, for that matter, anything Hell itself can dish out.
And even with Hell runs, I find that most of my deaths are hubris- or stupidity-related. For example, a couple days ago, I had gotten as far as 4-2, and had just unlocked the golden door, but declined to go through right away because (I thought) the path from the level entrance to that exit had been too quick, too easy, and I wanted to explore that floor a bit more. I wound up getting myself killed going after a crate. DX
(I have the same sort of problem in "real" roguelikes, too. =) )

Etherlords 1

It goes straight for the butt.

Also Marvelous Miss Take is pretty hard on you too.

Mortal Kombat 3 was pretty god awful.

I think the Super Nintendo Star Wars games were pretty terrible.

Black Market. Tiki trap setting of an exploding frog. A small explosion near a shop. "Terrorist!" Angry shopkeepers after me. Not my fault at all! Madness! ;)

ghouls and ghosts in the arcade - hurt my piggy bank
cookie clicker - hurt my finger
nethack.alt.org - hurt my head

Agreed, especially since I can't scum my nethack.alt.org save file.

That's how I feel. Oh man, remember when Jeremy sees the Master in pure pwnage? "What you must realize is that a true owner owns all games. If one wants to truly own. One must own in all games."

Great quote via a DS review. "It's not your character leveling up, it's you."

From what I hear, Wizardry IV: The Return of Werdna and Deathlord are pretty insane.

Stating the obvious here but the difficulty level in most of the early 80's arcade game was really high, i think you can generally see a natural reduction in the difficulty level of games as they progressed to the modern games of today. One of the most punishing games of the more modern era I think though would have to be S.T.A.L.K.E.R Shadow of Chernoybl.

Ignoring the first post where the criteria for 'punishing' is about as distinct as a thousand piece jigsaw puzzle of clear blue sky, I'd have to say Operation Flashpoint: Cold War Crisis. You get one save per mission, so treat it like you're down to your last condom in a room filled with the entire cast Game of Thrones cast.

If you haven't, try the black road in the Misery mod for Pripyat :)

Life

How about Tetris the Grand Master 3: Terror Instinct? (Also, TGM2 is also quite punishing.)

In TGM3's Master Mode (the main mode of the game), I believe only 7 people have ever reached GM rank; furthermore, when you start to play, you might get a demotion exam, and if you happen not to be playing well that day, you could lose your GM rank. Also, there's the requirement that each 100 level section (except the first and last) must be at most 2 seconds slower than the previous one to get the best rank, so if you get a fast section, it becomes harder to do so on the next section.

TGM3's Shirase mode is brutal. It *starts* with tetrads appearing at the bottom of the well as soon as they enter, and goes faster from there. It is *so* difficult that even the very best players in the world can't beat that mode consistently. Furthermore, if you don't reach level 500 fast enough, the game ends early (and meeting the time limit is much harder than simply reaching level 500).

It depends on which revision you play. Arcade games made by Japanese companies tend to be set to eat quarters outside of Japan.

Empire Strikes Back on the gameboy (and probably other systems). I think maybe I went past the first level once?

While I wouldn't say it's indisputable, my vote goes for Oni. The first level is pretty easy, but during the second level you get to a point where you have to take down about a dozen bad guys, with minimal ammo and hypo sprays,(items that heal you) then if you manage to do that, you have to take out several more bad guys, all armed with fully automatic machine pistols, with out a check-point to save your game anywhere in between. Add to that the fact that you can fall into vats of fluid which is an instant kill, while executing throws or kicks and you get one of the toughest games I've ever played. This game frequently forces you to use melee attacks against gun wielding foes (who are very intelligent and can hear you if you make the slightest sound) by the way, since you are given minimal ammo from the start and need to save it for the really tough foes.

BORDERLANDS 2: Lynchwood Station is by far the best designed level in the game, and brilliant in design, but 90 percent of the game design punishes the player. The Caustic Caverns, why is it that after opening the gate the first time by the entrance does it not stay open (even though the cart gate stays open) and I have to rerun the entire area for one thing. This is often the case. The vertical levels are all brutal if you jump off early or want to go back for one minor thing it is a massive slog and most likely the enemies have respawned so it is best to just save, quit and restart so you at least get the loot chests back if you have to fight it all again anyway. Everything is always the most tedious and obnoxious way to get somewhere or get some item.

The enemies are tedious. Most of the enemies you just can't shoot or attack. and not because they have good attack patterns, they are just crap of you can't attack from the front at all Loaders that deflect bullets with spinning props and metal shields, and shield loaders that deflect everything along with the flying crap that recharges and heals everything. Spiderants that can only take real damage from behind. They also require you carry a massive amount of different weapons. Why can't elemental just be a bonus? Why is it I need to have shock weapons for shields and some enemies, fire for others, caustic for loaders, etc. I feel I am always punished - that's a really awesome fire sniper rifle you have, but f-ck you, it is worthless here.

Shields are pointless. Every enemy basically one-shots a shield. The only reason to even use a shield is for whatever bonus is attached as the shield part has no value at all.

Oh yeah forgot, the random stupid quests that make you kill things a certain way or garbage enemies. Nothing like having to kill a bullymong with a melee attack for no reason, or shoot down stuff. The irony of how bad all these designs are is that Gearbox openly knows the designs are pure sh*t in game by stating "You will learn to hate them" The sign that reads "F*ck you" when you get into the area with the enemies that turn invisible or when Sir Hammerlock says "for no good reason" when he requires you to do the quests in the dumbest way possible. And I really like when I am trying to let the bugs grow to become badass bugs but Mordecai keeps shooting the larvae dead. Brilliant idea, putting a quest in an area that requires you to let an enemy level up while the NPC keeps killing them before it can happen.