The game is very good at this, despite having a mediocre translation. The first one that comes to mind is the ending, but there's also the goat in Eklemata, Elle's Heroic Sacrifice and the death of Royd and Fyda.
For this troper, during the Playable Epilogue, what really hit him was the kid looking at the pond: at the beggining, before opening the Pandora Box, the kid at the pond says the fortuneteller told him the image on the pond was the future, explaining to him why he was seeing so many high glass towers. Then, in the epilogue, he just says that he can't see anything on it anymore...
In the same part, after hearing throughout the story the same line about how "the unnecessary people will die, and all others will live forever", the shopkeep simply stating that "there isn't a single person who is unnecessary" is just...
Elle breaking down and crying at the beginning of the game because she fears that she would not see Ark again. She's completely right.
This game got me teary-eyed so many times. There was the moment when I learned that I couldn't talk to animals anymore, when Leim rescues you and when I realized, that after basically creating this whole world and developing the towns (and buying my character an apartment in my favorite town,) I had to leave it.
