Fluttershy's extended singing of her "Hush Now, Quiet Now" lullaby to Lockwood, helping him fall asleep when he awakes in terror at turning into a zombie and kill everypony, is extremely touching and shows just how much the two care about one another.
Shroud's send-off courtesy of Silvertongue in Chapter 25 involves him wiping her memory of the past few years and filling them instead with negative feelings about her job and the strong desire to leave the city she's lived in all her life. The reason this is truly touching is because we've seen how he's treated his other subordinates when he no longer had use for them (read: murder), so seeing him let her go is a sharp contrast and shows he has a heart. He even mentions that he wants her to live out the rest of her life in peace away from the horrendously chaotic New Pandemonium. Her goodbye to him is also pretty heartwarming.
It's especially powerful because of Silvertongue's attitude in the scene aswell. He seems genuinely sad to see her go, and says that he considers her his second most loyal servant (the most loyal being one who literally HAS to work for him because of magic). He even gives her a few moments of respectful silence after she's gone before carrying on with his business.
Despite the reason why they're all doing it, the Mean Six having a great big group hug at the end of Chapter 25 is touching. Of course, then you remember that they're all uniting as a family to murder the Mane Six, so...
Chapter 26's opening is a rendition of Rainbow Connection, sung by Pinkie Pie. Rainbow Dash is emotional about it and hides it poorly, and Pinkie reveals it is hers and Dash's song. The others are all touched by the rendition and by its meaning.
Chapter 27 features a big group hug delivered by the hero party to Tick Tock, accepting her fully into the group and forgiving her for her attitude before in the fic. Tick Tock is legitimately touched by the gesture. Said group hug is almost ruined when Briarthorn joins in.
Chapter 27 also features a little bit of bonding between CuraÁao and Havocwing after the former reveals that she blames herself for not being perfect enough to keep Insipid in control, showing just how much she has grown to love and care about her sister.
"...For another long moment, Havocwing gazed past her sister at nothing in particular, unfamiliar with what she herself was feeling. She actually didnít want her sister to cry. She realized she didnít want to lead if she had to see her family like this to get the chance."
Havocwing was this close to losing it in that scene. Her voice was shaking and everything. Really, the entire development of Havocwing's character post-25 is astounding, with her struggling to cope with her strange new feelings of compassion and responsibility, and discovering just how much she loves her sisters.