Father Raymond's murder, especially considering he was the only one who acted like a true father for Bear and Fish.
The Denniston boys' backstory in general.
In Black as Night:
Jack Fairston regretting how badly he treated his children.
In Rapunzel Let Down:
Raphaela losing her barn cats. After we see Patterson feed the live kittens of a new barn cat he's just killed to his vicious Dobermans. God only knows what he did to the poor previous ones before he got the dogs.
Hermes getting brutally beat up- twice- and sexually molested in prison. When Father Knopff visits, he asks him to sneak in a razor so Hermes can slit his wrists and end his pain.
Hermes' general inner rage and pain in prison, his anger at God and sorrow for Raphaela.
Raphaela giving birth to twins! She's so happy with her babies and relieved they're all alive.
The Torrodes family losing their child. But a very happy Tearjerker of Mona accidentally reuniting with her baby sister. Even more touching is when Raphaela meets her father.