This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Fallout: Equestria
IN the ruins of Manehattan, a corpse is discovered in the Ministry of Morale's office clutching a Twilight Sparkle figurine. When a letter from a nearby computer gives context for what happened over 200 years ago... the full weight of the tragedy hits hard.
Worse, Pinkie was heartbreakingly close to having stopped the Manehattan bombing, her strike team halfway into the very building where the zebras had smuggled in the balefire bomb. Had she, a whole branch of her Ministry, and an entire large city survived, the Wasteland may well have been blunted severely in getting out of control.
And when Littlepip delivers Pinkie's last message to the Twilight!Alicorn, 200 years after it should have arrived. The waterworks come then as well.
"All of Equestria Mourns Big Macintosh, Hero of Shattered Hoof Ridge"
The story of Stable 29. All the deaths, including the deaths of kids, with backstory so that they're not just meaningless. A pony's kid gets burned to death by plasma and he'd just gotten his cutie mark...Another was getting her stitches out and was planning her daughter's cutecenera...another couple's baby, suffocating in another room because of the fire suppression system. What makes it even worse was because the entire thing was started by another pony getting his colt a bebe gun for his cutecenera party. Something so innocent being devolved into something so horrible...
Just think if you missed a shot in the beginning of Fallout 3.
The last half of chapter 20.5(Technically Canon) had me bawling like a little girl.
Spike. Our favourite dragon goes to sleep for a while, as dragons are wont to do, only to wake up and find out he's lost everything. If your heart doesn't break when he's talking to Littlepip about it, you have no soul.
Plus there was the audio recording Littlepip is shown in the sealed off rooms of Tenpony Tower. The memory ends with Spike and Twilight having an argument, and Spike leaves it by basically saying "I'm gonna go take a nap! Come and find me when you're the Twilight I know and love! What makes it even worse is that that particular nap may very well have been the one he had been taking when the megaspells hit, making that possibly the last thing he said to Twilight.
Xenith describing how she's lived the majority of her life doing exactly what she's been told to do just to survive is horrifying (most of it amounting to "don't talk, hide" and keeping a low profile); but to the point where she feels she's unable to function independently, it becomes sad- before Littlepip became responsible for her, it was the slavers, preceded by her abusive husband, preceded by her own parents. It's why she's placed herself in Littlepip's hooves- she's a leader, but she won't abuse Xenith or knowingly place her in a dangerous situation. Be that as it may, it's a bit heartbreaking in the following exchange.
Xenith: I have never owned myself. I am not comfortable with the idea. I know this role. I can survive it.
Littlepip: I may be responsible for you, as you say. But I am not a slaver. I do not own you.
Xenith: And for that, you are better than all the others. But still the fact remains that I do not know how to live being responsible for myself.
Steelhooves returns to Canterlot, and while paired with Littlepip he comes across the very hoofprints he made where he ceased to "live" in the conventional sense. He begins to remember "the day Equestria died", recounts the details of the megaspell attack on Canterlot, his failing relationship with Applejack, his futile attempts to salvage it, the moment the two become separated after Cloudsdayle is hit and she leaves to check on her family- and it's then that, despite the fact that Steelhooves never takes off his helmet and despite the fact that his face is covered, Littlepip realizes that her adamantly stoic and expressionless companion is actually crying. It's deeply sad and horrifying to experience a calm yet emotional breakdown from someone that barely expresses any emotion whatsoever, and just like Littlepip, it's difficult not to have your heart go out to him. It's worse for Littlepip, as she has no idea what to do.
Littlepip: I wanted to hold him. To comfort him somehow. But I knew he wouldn't be able to feel it. That armor of his separated him from the rest of us. All I could do was be somepony who was here and who could listen.
In Chapter 35, after the massacre of Arbu, where Littlepip goes on a murderous rampage that leaves nearly everypony dead after realizing the inhabitants are all cannibals, Velvet Remedy and Steel Hooves side with Littlepip's actions, Xenith is on the fence understanding that anypony in dire straits would do what they had to if it meant survival; but Calamity is torn, as he can't justify what the party has just done. When one of the settlement's last (and grateful) survivors tries to show him a ledger containing all of Arbu's victims, Calamity refuses to read it, insisting that Littlepip made the wrong decision... and then suddenly tearfully hugs her, well-aware that what she's done must be tormenting her, that she possesses a good heart, "an' if that heart cries out in pain an' rage an' fury, then Ah've got t' believe it's fer a good reason", admitting that he's lived long enough in the wasteland that such atrocities have left him jaded. His entire tearful response speaks volumes of how cruel the wasteland can be, and how it can wear down even the best, well-intentioned ponies like him, who face such atrocities to a numbing degree- perhaps made all the more painful since he's seeing his best friend suffer so severely from that cruelty.
In Chapter 37 we find that Rarity used the Black Book to have her soul cut into 43 pieces, 42 to the figurines featuring the mane six and 1 for herself. This is so that her friends would go back to being friends. Its even sadder when one realizes that she might have been successful if the megaspells haven't fallen.
Chapter 39. Just... Chapter 39. Let's see, the Pegasus Enclave come down and obliterate the Canterlot Ruins, killing all the Ghouls living there INCLUDING Twilight's mom, they pretty much begin a genocide campaign against Friendship City just to get to ONE Dashite, Steelhooves is DEAD, and Velvet Remedy left the party, disillusioned and heartbroken, finally reaching her limit from all the horrible things she's seen, done, and seen Little Pip do. Actually, this might qualify better as a Wham Episode.
What makes Velvet's breakdown is that, in the end, she's absolutely right. Littlepip did slaughter thousands of children and other noncombatants just to kill the Goddess. She did cause the Enclave to invade by using the Megaspell. She did indirectly cause Steel Hooves' death at the Hellhounds' hooves.
A specific scene in Friendship City- Enclave soldiers begin looking for the Dashite they've been ordered to locate and tell civilians they'll be rewarded if they help. One pony outright refuses with a solid "Fuck you!", which results in said pony and those who try to run being turned to ash. It gets worse when Littlepip spots a terrified filly hiding. Littlepip tries to approach to comfort the filly- the filly spots her, screams out "Hellmare" in terror and tries to run for it. She's turned to ash. It's made worse by the context in which the scene happens- the filly only ran from Littlepip because, by this point, she's gained infamy for slaughtering almost the entire town of Arbu in a rage, after discovering the adults were cannibals that murdered other ponies and fed them to travelers- while many ponies don't blame her for her actions, a significant portion (particularly the survivors) does. The filly in question was an orphan from Arbu who saw Littlepip go berserk and who probably even saw her kill her parents- if Littlepip had stayed away, she might've survived, and Littlepip knows this. It affects her so badly that she gathers the poor filly's ashes, trying to find something to put them in; Calamity, who is barely able to keep together on his end as it is, has to physically slap her to bring her to her senses.
Calamity: Ponies lives are countin' on ya, Li'lpip. Ya'll gotta pull yourself together. Hurt tomorrow, help today.
Xenith being forced to keep Silver Bell from getting near Ditzy Doo due to her absorbing an extremely large amount of radiation from the Maripony explosion, therefore becoming lethally poisonous to anypony that is near her for an extended period. She actually has to write Silver Bell a message telling her to stay away because she's poisonous. Silver Bell's cry of "Mommy!" doesn't help. AT ALL.
A pre-war flashback to the zebra attack on Canterlot, where Fluttershy is flipping out at the zebras turning her megaspells into tools of destruction instead of tools of healing like she hoped they would. The worst part is is that she acknowledges that it's all her fault and that everypony (and zebra) is going to die because of her.
Out of all the Mane Cast, Fluttershy comes across as one of the most tragic. Especially with the implication she and Applejack were the only ones to truly survive the apocalypse. While Applejack had a peaceful ending, Fluttershy had to witness everything she cared and worked for get destroyed.
The undead schoolfoals and baby dragons in Canterlot. In fact, everything having to do with Canterlot and its environs is a potent combination of Tear Jerker and terrifying.
The Memory Orb of Pinkie Pie's last party shown in chapter 14. It starts of rather upbeat, with Rainbow Dash and Applejack acting like their regular selves, everypony having a good time. Then we witness an argument between Pinkie Pie and Twilight Sparkle. they too acting like their old selves. Until it's revealed to the readers that Pinkie was taking Party-Time mint-als, and wasn't really enjoying her own party. Twilight says that she's sick of lying to Celestia about Pinkie's condition. She then tells her that she wants the old Pinkie Pie back, and says that their friendship is over if she doesn't fess up. Pinkie Pie then reverts to Pinkamena as Twilight (and Rainbow Dash) leaves, but not before Twilight says the following:
"If you decide to be my Pinkie Pie again...really do...and need help, you know where to call."
Everything having to due with how the Old World died. We are shown, in agonizing detail, exactly how everything went to hell, how the characters we've spent five seasons knowing and loving were completely broken by a war none of them wanted, and finally how their lives were completely destroyed by both the war and their own mistakes. The final fates of Pinkie, Twilight, Rarity and Luna are especially heartrending.
Even Applejack, the only one confirmed to have passed away of natural causes, doesn't get off easily. One of her closest friends is murdered in cold blood by her own lover, who is completely unrepentent, forcing her to exile him. Her brother is killed in battle. Her sister dies of radiation poisoning. Even after she passes on, her legacy as a protector of Equestria is almost completely destroyed by the Steel Rangers' leadership who, in their opportunistic greed, spread lies about her painting her as an overly ambitious sellout and failure.
Rainbow Dash's fate is never revealed and she is Left Hanging. Ironic that the character who wanted to go down in history was completely forgotten. Word of God suggested Rainbow may have become a ghoul and lived on as a good samaritan, something which is adapted in Project Horizons.
Littlepip's reunion with her neglectful, alcoholic mother after saving Stable #2 from the Steel Rangers. Her mother barely acknowledges her daughter, goes back to drinking and claims she has suffered from the invasion. Littlepip feels utterly small and invisible in her mother's presence til Velvet slaps her mother hard and shouts that she has suffered nothing.