In the Rikti WarZone arcs of City of Heroes, Lt. Sefu Tendaji, the Longbow agent who's generally friendly toward you regardless of whatever other issues Longbow and Vanguard have, fills this role.
What makes it a wonderfully painful Punch isn't that he's built up nicely as a sympathetic figure, working first as an extremely useful ally and then as an honorable (if hard to defeat) enemy. It's that he isn't even killed for a good reason. He's not a threat, about to uncover the terrible secret behind the Rikti War. He's not an inspirational symbol of how enemies can team up to challenge a greater evil. No, he's killed because Nemesis is a racist. That's the point where Nemesis crosses the line.
The game gives us a new one in Issue 17: You're given a doppelganger who at first is an opponent, but then starts working with you on your missions. At the end of the arc, they're all alone fighting off dozens of clones of you while you're taking on the mastermind behind the whole mess. You win, but the fight takes its toll on your double; they stay behind to make sure the bombs they set go off, and you race to get them out... you're forcefully kicked from the mission just as you're about to reach them and everything explodes around you.
In the Wrath of the Lich King expansion in World of Warcraft. Any player, Horde or Alliance, who has experienced it needs only to hear the words Angra'thar the Wrath Gate.
Less so on Horde side, though. Alliance loses Bolvar Fordragon, the benevolent regent of Stormwind, who had been in the game for more than two years and had saved the player character from being ambushed by the dragon Onyxia. Horde loses Saurfang the Younger, who, unlike his badass father, had done nothing remarkable until the Wrath Gate.
Except that wasn't the only thing the Horde lost: Apart from the emotional significance of delivering the news of Saurfang the Younger's death to his father, the Horde must then confront one of their former racial leaders, Varimathras, who has been in the game since launch and even started quest lines for younger characters. The Horde falls under martial law, the Forsaken have to, well, forsake their home until Thrall, Sylvanas and Vol'jin can storm the Undercity with the player character (and any friends he/she brings) and put an end to Varimathras, removing him from the game permanently. And even after you tear one of the Horde's capitals down to cinders around the traitor's ears, you learn that it was still all for naught, and the Alliance king Varian Wrynn reignites the war that Thrall and the others have been fighting for years to prevent.
This is still a difficult quest line for the Alliance players who enjoy the lore and fleshed out story Blizzard has really put into this expansion. You first accompany Jaina Proudmoore on a diplomatic mission to Thrall about the events at the Wrathgate and find that both Jaina and Thrall are dedicated to creating peace and cooperation on both sides to fight Arthas. After you help Varian and Jaina reclaim the Undercity, Varian hears a warcry from Thrall for having defeated Varimathras and takes the fight on to Thrall and his soldiers. Wrynn then declares his goal to destroy the Horde once and for all. Jaina does stop him, but not before it's too late to stop the war. No specific player or NPC dies, just the hope for peace between the Horde and Alliance.
The Wrath Gate also has a.... different kind of Player Punch, specifically for Forsaken players. See, that bioweapon Putress is hocking at the Horde, Alliance AND Scourge? Yeah, every single Forsaken player had a hand in making that. There's a series of quests before you even leave the starting zone - called 'A New Plague', in which we assist the Royal Apothecary Society in the development of a new secret weapon(ized disease). When Putress roars DID YOU THINK WE HAD FORGOTTEN?, every single Forsaken on Azeroth went HOLY CRAP WE DID. It gets more evident once you reach Vengeance Landing and Venomspite, but it only sinks in after the Wrath Gate.
The entire Horde-side questline through Howling Fjord and Venomspite deals with the Forsaken apothecary's final preparations to bring this weapon to bear. If you ever did those zones, you were directly responsible for this.
The Wrath Gate comes back to haunt the player even further when one of the bosses in Icecrown Citadel turns out to be Deathbringer Saurfang. Yes, Arthas raised Saurfang the Younger after the Wrathgate incident to become his most powerful Death Knight and now the player has to kill him. Again. Alliance and Horde each even get their own versions of an in-game cutscene to beat the crap out of you even more:
Horde players are accompanied by High Overlord Saurfang — his father — when he appears at the entrance to the Upper Spire and asks his father to join him in service to Arthas. The High Overlord responds, "My boy died at the Wrathgate. I am only here to claim his body." before charging into battle. After the battle, Saurfang kneels over his son's body and weeps before carrying it to the airship to take him to Nagrand to be placed with his mother at the ancestral burial grounds.
For Alliance players, when the fight is over, the High Overlord arrives to claim his son's body, only to be stopped by Muradin Bronzebeard. Muradin is about to resort to force when Jaina Proudmoore teleports herself and King Wrynn onto the scene. Considering Wrynn and Saurfang's history, when the King tells Muradin, "Stand down, Muradin. Let a grieving father pass," every single Alliance player knows exactly how much a Crowning Moment Of Heartwarming this is.
And anyone who's played a death knight needs only to hear the words "A Special Surprise" for still another.
Night Elf Death Knights have it the worst out of all the races. For Night Elves, the target of the quest is their caretaker while they were still an infant. DAMN.
Worgen and Goblin are both pretty bad too. While other races talk about where your character was born, the Worgen reminds you about your life in slavery to Arugal and claims that if not for you, he would have died in slavery on the night the two of you escaped. And the Goblin as your best friend who insists that you were the only decent goblin he ever met and that he joined the Argent Dawn to honor your memory.
For many Horde players, if they can find her, delivering the news to Mankrik about his wife can be a sobering task.
For Alliance players, there's Emmy Malin. Emmy is a captain in Malygos' anti-magic army and is in charge of one of the ley line foci located in southwestern Dragonblight. Player characters have to kill her to get a ring necessary for reading and recording information stored in the focus she's guarding. When looted by an Alliance character, her corpse proves to hold a letter she had written to her father, detailing how she had been forced into serving Malygos and that she had been working from the inside to sabotage the corrupted blue dragons' plans. The questgiver tells the PCs that they shouldn't feel guilty as there was no way they could have known, and Emmy's father, an Archmage in Dalaran, even sends a letter later saying that he understands the actions taken by the PCs and forgives them . . . but damn. That's still a kick in the gut.
The same goes in Horde version for Ta'zinni, who had a similar backstory and of course another quest requires you to kill him as well. Converse to the Alliance equivalent, Ta'zinni's sister sends the player a letter swearing vengeance on whoever killed her brother, your exact role in his death being covered up when she was informed.
Thereby turning what just about every lore fan acknowledged was Arthas being handed an Idiot Ball into a geniusplan.
The Battle of Darrowshire. While we see why the Plaguelands is called Plaguelands, finding a ghost of a little girl is a completely different thing.
A good Punch (though not actually tear-jerking) comes with the unbelievably long quest chain (the longest in the game) in The Storm Peaks, where you basically reinvigorate a downcast Thorim to raze hell only to find out thateverything you'd done for Lok'lira the Crone, from freeing her to the end of the quest chain, was actually for Thorim's jerkass brother Loken. It's your fault that Thorim gets captured and corrupted. It's your fault that Veranus, a noble proto-dragon broodmother and Thorim's old ally, is tortured and transformed into Razorscale. This isn't a Player Punch, so much as it's a Player Instant-Hell-Murder.
In the old Duskwood zone, there was a very long questline you do for a nice old man living in a shack at the edge of the woods. His requests for things like ghoul ribs, plague flowers etc. aren't really that strange considering what else this game has had you do so far. And he only wants to make wacky voodoo charms to protect himself, right? Up until he hands you a note to take to the town mayor, informing them about the horrific abomination that he's created and is about to unleash on their town. Which so you kindly helped him to build.
Also in Duskwood is the saga of Mortimer Ladimir, the selfless paladin who spent his entire life sacrificing for the good of others, only to be caught by despair and corruption following the death of his wife and children. Also known as Mor'Ladim, the elite-level killer revenant who will appear out of the dark mists without warning to kill your ass while you're trying to complete quests in the eerie graveyard of Raven Hill.
As of Mists of Pandaria just three words: the Battle of Theramore.
And the Jade Serpent statue, which was to become the new Jade Serpent. The Jade Seprent herself, Yu'lon, tells you in a questline that it's been under construction for a hundred years, and she was ready to die and pass on her life force to animate the statue as the new Jade Serpent... and then the Alliance and Horde, despite having been shown repeatedly what happens in Pandaria when a lot of negative emotion is generated, show up and start a massive battle at the foot of the statue. Things rapidly get out of hand as stray fire from their siege weapons destroys the statue, releasing the monstrous Sha of Doubt imprisoned beneath it. What makes this especially gut-wrenching is that in previous quests, the player helps their faction prepare for this very battle, essentially meaning that YOU are an accessory to bringing doom to an innocent race of people, despite having claimed peaceful intentions when you first met them. You'll likely leave the Jade Forest wondering if you'll ever be able to look a pandaren in the eye ever again.
For Horde and Alliance both, "Breath of Darkest Shadow" ends with one. You're forced to watch as Garrosh nearly kills a pacifistic teenager and declares it to be a triumph for the Horde. The Alliance at least sees Anduin to safety; the Horde have to leave him there, comatose and broken.
The Reveal that General Nazgrim is a boss in the Siege of Orgrimmar.
In Vindictus, Ellis is a cadet who at first comes off as the "Oh I'm happy to be here" cadet for the royal army. After it's implied that the royal army was the provocation of a recently destroyed village he almost breaks at the mere thought that his ideals were not those of his army's, to the point of appearing sad for the first time. When he gets permission to examine the incident, he rushes off to the village to examine. The normally Cloud Cuckoo Lander old man realizes just how deadly that was, and warns you that you had better get over there fast. He promptly gets brutalized and then killed by a sadistic goblin warlord when you finally catch up to him.
The death of Gwynn, a fairly major NPC is the first chapter, gets killed at the end of Chapter 8 trying to protect Kheagan. She was a Defrosting Ice Queen, and one who was heavily involved in the plot. Her death emphasizes the seriousness of the storyline if nothing else. Even worse, her icon, the one that depicts she's in a location, sticks around for any sidequests uncompleted that might involve her conversation in the dialogue, as a constant reminder that she's dead now.
The entire planet of Taris. A Marathon Level and Bleak Level of the highest caliber, it's a sad mess covered in toxic waste, overgrown ruins, and rakghouls everywhere. Do you remember it from the first game where it was an active, albeit crime-ridden city planet?
Finding the logs of the Outcasts. Oh, hey! There were survivors due to your Player Character's "canonical" light side actions in that first game. Then, you find more logs...their shelter was in ruins. They ran out of vaccine and couldn't make more because the rakghoul virus mutated. The survivors held on for a few, pathetic generations until you find the last log where the final survivor speaks in broken, halting Basic. The few survivors that managed to survive disease, starvation, and rakghouls were rendered barren by toxic radiation. Congratulations, player. Instead of a quick death by orbital bombardment, you condemned them to a slow death by disease, starvation, rakghouls, and toxic waste. How about those Light Side points?
Finding out what happened to your PlayerCharacters from those first games. First game? You were Darth freakin Revan, biggest Badass in the known galaxy! Uh...no. Turns out, Revan went to Unknown space and got his ass handed to him by the Sith Emperor - that's why he made the Face-Heel Turn and began conquering worlds, hoping to become the Emperor's Starscream by making the conquered Republic his private fief and betraying him later. When Malak decided to betray Revan first and the Jedi got lucky, the plan fell apart. Revan later remembers this, but instead of warning his loved ones or the Republic, or even making plans to document the threat, he goes charging in alone and without warning to stop the threat...leaving Bastila knocked up and facing everything from assassins on her tail to a sentence of exile with no support. What the Hell, Hero??
Second game, you played the only Jedi who was strong enough to tell Revan "NO" when it came to betraying the Republic, and strong enough to go back and face the Jedi Council for going off to fight the Mandalorians. By endgame, a wave of the wrist and whole armies were getting knocked on their butts. Takes out her Evil Mentor who wanted to destroy the Force itself What happened? Goes along with Revan on the idiotic scheme, gets stabbed in the back by Lord Scourge, who ends up rewarded as a hero and bunking on the Knight's boat.
And then, the flashpoints that show the final fate of Revan. He was captured by the Emperor and used as the Emperor's favorite Mind RapeChew Toy for the next three centuries. Revan claims he tempered the Emperor's hate and convinced him to declare a truce with the Republic. Considering that the Emperor is an Omnicidal Maniac nutcase who doesn't give a whit about his own Empire and wants the entire galaxy (save himself) dead, it's just as likely that a war of attrition plays right into his hands anyway (it kills off lots of people, and keeps his Darths busy so they don't gang up on him) and Revan's just deluding himself. The Republic strike team frees Revan, the Empire claims the Emperor let him go...there's probably some merit to the latter claim as the Imperial strike team finds him on a Rakata droid factory called The Foundry, clearly insane, and amassing an army of killer droids (including a rebuilt HK-47) that will wipe out about 98% of the Imperial population (and, considering the amount of side-swapping in that universe, an equally large chunk of the Republic). This, again, would play right into the Emperor's omnicidal plans. And it's up to a team of Imperials, who are Noble Demon characters at best who have to charge in and put him down like a rabid dog. his last line even echoes Malak pathethically as he dies for an extra twist of the blade.
One Star Wars: The Old Republic one that has nothing to do with the backstory: Playing the Bounty Hunter, you come back from your first successful mession as a member of Braden's stable to find the Bounty Office in ruins, Braden and his partner dead, and the sweetheart Mission Control Mako devastated by the loss of her adoptive family.
Star Trek Online has the Romulan captain mission "Mind Game". After accidentally hoping through an Iconian portal into General Hakeev's ship, he captures you and Mind Rapes you into becoming a member of the Tal Shiar. To make sure you're good and brainwashed? You're sent to do certain errands - you're forced to kill a member of your crew it isn't, but you don't find out until after the test. But, you still killed someone in cold blood, construct a Thalarion weapon and use it on innocent Epohs (essentially cute and cuddly creatures), then implant Borg tech on a captured Romulan. Even worse, you get the option to resist, but when you use up all of your resisting options, you're forced to do these options. Even when you try to save someone by killing them, the game refuses to let you do so. You helplessly watch as your character does some unspeakable things. On the plus side, this makes your final encounter with Hakeev and Empress Sela so much more satisfying.
WildStar has the Calmwater Commune in Ellevar. In exchange for Eldan Artefacts, you deliver supplies to them and help around the community, by collecting food, earning the trust of the Hydro spirits, and even playing kickball with their children! Unbeknownst to you, the supplies are poisoned. You get revenge against the man who did it, but then you have to go and kill the rest of the Commune for your own safety.