This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / The Pendragon Adventure
Black Water: Kasha's death. This strong, brave warrior is reduced to a lost kitten as she approaches the brink of death. Bobby is about to leave to try and get help, but she begs him not to go. He looks at her, and realizes that what she needs at that moment is someone to stay with her. So that's what he does, sitting with her and holding her paw until she's gone.
The Quillan Games: The destruction of Mr. Pop. An entire civilization's culture, all the work that went into caring for it and preserving it and keeping it safe and hidden, the life of the rebellion, burned.
The Pilgrims of Rayne:
Courtney's confrontation with Mark on the ship, when she remembers how Mark supposedly died, realizes that she was the one to kill him, and pulls a gun on him. Thankfully, it doesn't go the tragic route, but Courtney being driven to such desperation is just awful regardless, especially seeing how the two have slowly become good friends throughout the course of the whole series.