This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / The Elements of Harmony and the Savior of Worlds
A flashback of when Celestia was forced to banish Nightmare Moon. Before she did, Celestia tried to reason with her by reminding her of Megan, Danny, Molly and the G1 ponies, but Nightmare Moon doesn't care about them (anymore).
The Mane Six's realization that most of Megan's old friends are long gone.
Megan crying at the memorial for Wind Whistler is rather touching stuff, considering she was her favorite friend.
Megan: "Wind Whistler, my old friend. I'm so sorry I never said goodbye. What you built here with your four hooves, it's greater than I ever dreamed of. I just wish...I wish I could t-tell you, to your face.”
Luna is afraid to reunite with Megan, Danny, and Molly, because they might hate her when they learn about Nightmare Moon. Also, she blames herself for Danny's injury.
Danielle falls on her knees crying in United We Stand chapter 8, after trying to act brave as her mom would have in the last chapter.