Tear Jerker / The Changeling of the Guard

• The backstory of the Nymph and the Nursemaid. Long story short, the Nymph was identified as "colorblind", and so Chrysalis ordered that she be executed for her disability. Instead, the Nursemaid smuggles her into Idol's care and then voluntarily commits suicide so that she can't obey Chrysalis' Orders to hurt her former charge.
• In Chapter 48, Idol's confession of his despair from Chrysalis' Orders and what they mean for his long term goals is heartbreaking to read.
  "...I love my queen. I cannot not love her. She is the Queen, and she knows best." A tear escaped me. I could grieve, at least. "...But I think I hate her a little, too. In this too, I have failed."
• In Chapter 55, the half-maddened exile who reveals she was forced to flee because Queen Chrysalis wouldn't let her have children. To clarify; the first two eggs she laid, the Queen declared they weren't fit to be incubated. So she mated a third time and then tried to hide her eggs — a huge no-no in changeling culture. Chrysalis found the eggs and, despite them being far along — implicitly close to hatching — she destroyed them before the exile's eyes. The mother attacked her in a fury, and then Chrysalis exiled her, placing her under Orders... not to never breed, because that wasn't cruel enough: if the exile ever has eggs that she thinks of as "hers", then she is irresistibly compelled to throw them against the ground and trample them into mush. As she bitterly notes to Idol, she can't even buy chicken eggs in the market without it triggering.
• Also in Chapter 55, Idol introduces the aforementioned exile to the Nymph, hoping the two would be good for each other as a family unit. Instead, the exile bitterly rejects the Nymph, denouncing her as "broken" and an unworthy substitute for the biological child she is obsessed with having.
  "I want my own. What care have I for this pitiful thing?" She laughed, mockingly. "By the Queen's commands, I cannot even purchase eggs at the market. If I buy a dozen chicken eggs, if I ever dare think of them as 'my eggs', I am compelled to cast them to the cobble and crush them all. It will be all I can think of until the deed is done. By all means, give me one that the Queen has deemed better than my own and still proven flawed." The grin she gave me was wicked, chillingly so. "The Queen will get her back, I assure you."
• Yet another Chapter 55 example; Mothchaser finally gets into Idol's bedroom, and they begin engaging in what she excitedly thinks is foreplay... but then she realizes it's just a massage. Idol is forced to tell her that even though he likes her, he's simply not capable of sexual activity with her, so upset for the distress that he is bringing her that he even manages to wriggle around his Orders and reveal to her that he's not a pony so as to try and explain that she is not to blame for his lack of response. And all the while, he privately reveals he's actually as hurt by his inability as she is, in a Call-Back to the aforementioned reveal from Chapter 48.
• In Chapter 65, Idol finds himself suffering a major Identity Breakdown thanks to a combination of the trauma of turning on his former Queen Chrysalis and "outing himself" as a Changeling to Shining, and the mental damage done by both his near-death experience and Chrysalis' clumsy efforts at rewriting his mind once she'd rebuilt him. When Cadance comes to see him in the dungeon, Idol essentially explains to her that he isn't entirely sure if he is Idol Hooves anymore, or if he can ever be Idol Hooves again, such is his mental disorientation. Cadence herself starts crying, then vows to find some way to "fix" him before leaving.
• Chapter 69:
  • The state of the Crystal Empire is just so incredibly broken. It turns out that Sombra once pretended to be defeated... so he could wipe out anyone who dared to step forth to try and lead the Crystal Ponies once they fell for his trick. Shining Armor notes it's going to be an incredible uphill battle to reconstruct the Empire without having them simply be subsumed into Equestria, they are that emotionally fragile.
  • Cersus' drastic emotional breakdown when she finally admits just how alone and frightened she was during the invasion, and then afterwards when Idol vanished into the dungeon.
  • Celestia's tearful confession to Idol that she always wanted to be a mother, but somehow she never found the time — and now, as she sees it, her position as one of the Diarches of Equestria prevents her from ever fulfilling that dream. She's tried to channel her maternal urges into her personal students, like Twilight Sparkle, but it just isn't the same, as there's always that gap between them.