Phoenix Wright: Ace Attorney: in Trials and Tribulations case 5, when Dahlia Hawthorne starts cackling about Maya's apparent suicide, and how she can't be punished for it because she's already dead. Even given that you've most likely figured the true plot out already by this point, the anger generated by this scene is part of what makes Mia and Phoenix's resultant Hannibal Lecture such a Crowning Moment of Awesome for the series.
Dahlia is also responsible for another Player Punch earlier:
Mia's death near the beginning of the first game works this way too. It's a bit different from this trope's norm in the sense that you don't really get a sense of how awesome she was until after she dies. In any case, Redd White is quite likely the most hated villain in the series who isn't a final case villain.
Planetarian It comes to punch you in the eye when you're already attached to Yumemi/Reverie
In the Heaven's Feel route of Fate/stay night, you're forced to select the choice that kills Saber in order to obtain the True End.
Choosing to let Saber live has fatal consequences for Rin, who, as a result of Saber's timely intervention, gets absorbed by Sakura. She then proceeds to inflict a re-enactment of her experiences in the Matou household on Rin, and the utter horror of the scene is compounded when Sakura lets Shirou know in an arrestingly deadpan manner that Rin was a virgin, and that she's "already crying on her first day."
Doesn't change the fact that it's difficult to stomach killing off Shirou's first love for seemingly no reason. The related bad end is something of a Diabolus ex Machina, coming the hell out of nowhere.
If that wasn't already bad enough, the True End route also has Ilya sacrifice herself; this is non-negotiable on your first play, and the worst part of it all? That innocent little jingle of hers plays as she does so, increasing the tear-inducing factor of the scene by over nine thousand.
Worse than this, when you do get the choice, choosing to prevent Ilya from sacrificing herself leads to the Normal end, which apart from being exceptionally depressing doesn't mention Ilya at all, implying that she probably returned to her castle to live the rest of her (short) life alone, since Shirou is dead and Sakura is far too depressed to possibly look after Ilya.
CLANNAD: When Nagisa and Tomoya want to confirm Fuko's situation by trying to get her older sister Kouko to meet her, Kouko ends up staring straight through Fuko and she says to Tomoya, "That girl stopped breathing yesterday."
And then there's Nagisa herself who dies in her good ending from child birth - this is necessary to get the best ending (i.e. saving Nagisa).
Early on in the survival horror visual novel Corpse Party, Naomi and Seiko unwittingly step into a pile of gore. It's played for dark laughs, but later on, we find out that the body belongs to their friend Mayu.
Katawa Shoujo: Basically every bad ending is this, and the game really chews out the player for it more than Hisao.
There's especially the bad end in Shizune's route. How do you get it? By cheating on her with Misha.
Danganronpa has the obvious gut punches whenever one of the characters you've come to care for turns out to be the next victim... or the murderer.
Chihiro's final Free Time event, where Naegi has no choice but to recommend Chihiro ask Mondo for help getting stronger. This is only accessable in a New Game+, so the player knows what will come of this...
Similarly, Sakura's final Free Time event reveals that the person she could never defeat was Kenichirou, her boyfriend, who was terminally ill. Given only six months to live, he fought to survive... yet enough time has passed before the events of the game that he's likely long since passed on.
Muv-Luv Alternative is chock full of these and when you start feeling like you've gotten used to them they just blind side you anyway. It probably really starts all going to hell when instructor Jinguuji dies horrifically and it just keeps getting worse and worse from there.
shortly after that Takeru panics and runs back to his original world and in so doing indirectly brings about Jinguuji's horrific death in that timeline *again* and it gets worse still as everyone who ever cared for him starts to forget him, even Sumika who loves him dearly. Then Sumika gets in a terrible accident that very nearly kills her, again indirectly caused by Takeru fleeing to the Extra world.
following those events Takeru essentially gives up and wants to die but Yuuko helps him get back to the alternative world, giving him hope he can fix everything again if he goes back. When he arrives there he learns the true fate of Sumika in the alternative world which was incomprehensibly horrific. but she was still alive as a brain in a jar, until recently. now her soul got ported into a quantum computer (killing the brain in the process) and her existence now forms the core of the last hope of human victory over the BETA. Takeru just has to get her back into... working order. Not an easy task with her mind so utterly broken by the trauma she experienced followed by 3 years of living as just a brain
Things start to look up a little and Takeru's first big mission to Assault Sadogashima's hive in a huge offensive goes very promising, but in the end his captain, Isumi, has to sacrifice herself to save the day.
After the aftermath of that big mess settles down Sumika seems to be doing very well but unexpectedly rejects Takeru when he confesses his love for her. She also convinced Yuuko to remove him from his unit and stop him from piloting a TSF ever again, dashing his hopes on saving the world and undoing the damage he caused in the Extra world.
In Virtue's Last Reward, if you betray Luna in the third round on her route, not only does this lead to a bad end, Zero III unexpectedly shows up to chew Sigma (and by extension the player) out for it.
In Quark's route, if Sigma gives into Dio's blackmail and allies with him, Dio betrays him, ensuring his own escape and also leaving Sigma minutes from death.
In No One Has To Die, Troy didn't light the fire - he only claims to be the arsonist so that you will kill him and save someone else. Thanks to a twisted kind of "Groundhog Day" Loop, he's had to watch everyone else die in the fire five times just so he could live, and he's desperate to make sure someone other than him survives. The only way to discover all of this is to put him through it again.