In the bad ending of Fatal Frame II, the main character chases her possessed sister into the caves under the village, but will find herself forced to undergo the barbaric ritual of the village that you've been (indirectly) suffering the consequences of all game: Mio chokes Mayu to death, turning her spirit into one of the Crimson Butterflies that have been fluttering around the village. And the worst part? This will always happen to you your first time through the game. The good end isn't even available unless you're playing on a higher, unlocked difficulty.
The real Player Punch? This is the canon ending. And the very fact that the deliberately brutal and emotionally cruel sacrifices are supposed to be the right thing to do in the games' setting was a pretty big Player Punch.
Even if you have already been spoiled on the truth about James in Silent Hill 2 or picked up on the disturbing implications of the anvilicious foreshadowing, the inevitable reveal is still a kick in the gut. (L0rdVega's Blind Playthrough is the perfect example of this. Listen to his muted "I knew it" at 3:12 and compare to how mercilessly he'd otherwise been mocking James' incompetence in other videos.)
Silent Hill 2 actually plays with this trope in several ways. In addition to what was described above, the game twists the knot on this trope with Maria, whose presence results in at least threePlayer Punches — and, in most cases a fourth, which you yourself must deliver. Alternatively, in the case of a particular ending, instead of Maria dying a fourth time, the player encounters his own wife, who is (sort of) alive and (completely) furious with you, and after you've spent the entire game ostensibly trying to find her, only to discover that you killed her yourself, you have to kill her again.
And that's after you've had to kill Eddie. Though, granted, he wasn't very sympathetic, but Angela was, and you had to just watch as she walked away into hell. Having some actual people around just to make terrible things happen pretty much highlights what a twisted place Silent Hill is.
Then, of course, we have the "In Water" ending, where James commits suicide, and the full text of the letter from his wife (which was a posthumous note) was read by the VA... and we find out that she wanted him to live his life.
In Silent Hill 3, Harry is killed specifically to piss off Heather (and by extension the player). Vincent's death is also a pretty powerful Player Punch, the charming bastard.
Agentjr discovering Harry's body in his playthrough is pretty much how most Silent Hill fans felt. The aftermath to the player punch is also very bitter.
The original Silent Hill also has Harry pushing away and running from a desperate and horrified Lisa Garland.
The Good ending of Silent Hill delivers a huge Player Punch by making you kill Cybil, only to later find out that the innocuous red liquid you picked up in the hospital and forgot about four hours ago could have saved her.
The twist ending to Silent Hill: Shattered Memories reveals that Cheryl was the protagonist all along, and that Harry has been dead throughout the entire game.
The endings of Silent Hill 4 — all of themexcept for "21 Sacraments", which is an entirelydifferent flavor of Player Punch. Walter falls to the ground, and as a pool of blood begins to surround him, he reaches one arm up into the air and simply says "Mom...?". After that, you're treated to another cutscene of younger Walter knocking on 302's door, asking to be let in, and suddenly stops, stands motionless for a second, and then crumples to the ground and disappears.
In Dead Space, you find multiple logs from Temple and Cross, two people who survived a while and are built up as quite sympathetic as you hear from them... but they're probably already dead. You find out they're not, just in time for the evil Mad Scientist to brutally kill them while a security lockdown keeps you from doing anything but watching.
Even worse: Nicole is dead. Sure, it was foreshadowed heavily, but finding out that Isaac's entire reason for being there, the one reason he kept going, had killed herself before he even arrived and the rest was all just a Mind Screw kinda hurt.
Hell, even Hammond's death. It's easy to go back and forth on him throughout the game — is he a good guy, is he a backstabbing bastard like Kendra is saying? But that tends to fade after he puts his all into helping you get the ship back together and encourages you to keep going, and even nearly dies from toxin inhalation. Then you finally meet up with him again, only to watch him be viciously torn apart by a Brute.
The original Resident Evil and the REmake has this with Richard. The original had him dying even if you got the serum for him in time, and in Remake, he lives long enough to get eaten by something. Chris's scenario is the worst of the two, as you can actually watch over Richard while he sleeps.
Even worse if, when playing Rebecca in Chris' story (when Chris is poisoned and needs serum), try to take a lot of time (say, ten minutes) to get the serum and come back. The cutscene speaks for itself.
In Resident Evil Code Veronica, there's a romantic subplot taking place between Steve and Claire. Just when you think the two of them have earned their happy ending, Steve is kidnapped and injected with the T-Veronica virus, causing him to mutate into a giant killing machine. The effects eventually wear off, but Steve dies shortly after, having just enough time to confess his love to a heartbroken Claire.
In the case of Eternal Darkness, maybe this could be called something along the lines of Broke Your Arm Punching Out CthulhuAnd Cthulhu Punched Back, as eleven twelfths of the game take place within the chapters of a book of the fight against an Eldritch Abomination God on the rise spanning history, each chapter focusing on a different character's efforts. Every one of these characters was a perfectly ordinary (essentially) and usually quite lovable person who just had to get mixed up in the whole thing, often by being in the wrong place at the wrong time, and even though they usually strike a blow, it's at a dear cost. Say, life or sanity. Some of the hardest punches are when Ellia, a dancer seeking entertainment in a temple to Kali, finds out that the temple houses yet another Eldritch Abomination God and is made to hold its essence — which keeps her from dying even when she's killed for knowing too much, the last bit not something you know until another character over a thousand years later finds her remains and she passes it on to him and Anthony, a messenger for Charlemagne, gets blasted with a curse meant for Charlemagne that slowly turns him into a zombie and, long story short, by the time he gets to Charlemagne to tell him of impending treachery, he finds out he's too late and is left zombified, unable to die, and alone for centuries until the player, as yet another character, is forced to put him out of his misery themself. And he still whispers "Charlemaaagne!" and lets out this pathetic moan now and then, too. That Anthony is played by the wonderfully talented Cam Clark helps.
The Lovecraftian themes of Eternal Darkness lend themselves well to the player punch as only four of the playable characters come out merely scarred for life with most of their mental faculties intact. For another example, there's Paul, the very sympathetic priest, who has to fight Anthony later as an enraged zombie. He prays for Anthony's soul afterwards which, although arguably futile given the Lovecraftian universe the game exists in, helps bring some closure to poor Anthony. Then what happens? You get to the end of the chapter and meet a giant... thing that either eats Paul's head or makes it pop like a balloon and there's not a damn thing you can do about it because it's a cutscene. Peter Jacobs gets to take that blasted head-eater down later, thankfully.
Penumbra: Overture has the player crawling through a dark, crumbling mining complex filled to the (cracked) rafters with Eldritch Abominations and once-living creatures, all the while being led by a seemingly kindred spirit known as "Red" who is clearly insane from isolation. However, he befriends the player in a one-sided way, and you'll likely get attached to him as well. However, in the final moments of the game, to open the door and move on, the player must incinerate poor Red, who is laying in an oven, to get the key to move on, as Red had been suffering alone for so long, and had convinced himself, in his madness that he could not take his own life, as "That was against the rules". The second you get your guts up to start the machine, he screams bloody murder. Cue My God, What Have I Done?, Heroic BSOD on the PLAYER end, and ending it all with a Tear Jerker from being Player Punched so hard.
It gets worse in the sequel, Black Plague. There, you befriend Amabel, a scientist that needs your help to escape and find a cure for a virus that's going around... which, incidentally, infects you and results in Clarence's snarky comments echoing in your head for the rest of the game. But the topper is when you finally reach Amabel, and are greeted with an Infected instead, which you then have to kill by dropping a crate atop it... only for Clarence to say "Gotcha" and reveal that it was Amabel the whole time. The exact phrasing used in that scene can be found under Nice Job Breaking It, Hero in Penumbra's page.
Not to mention that any Genre Savvy player that kept their wits about them knew it was her, which only makes the Player Punch that much harder.