This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Golden Sun: Dark Dawn
In Dark Dawn: the fate of Champa. Its one of two towns that reappears, mostly unchanged, from the previous titles, but thanks to the Grave Eclipse, it's full of shadow mist and dead bodies. The people who are left? They spend their time burning their houses, along with whatever else they can find, to keep the shadow monsters from attacking Obaba. Perhaps worst of all, there's no indication of what happened to Chaucha. Briggs mentions her, but we never get to find out if she died or fled or is shoveling furniture onto the bonfires or what.
Another one for Dark Dawn. Take a look at Volechek. After all the things he has been through, it's hard to not feel some sympathy towards him. He is a king of Belinsk, a kingdom made up of beastmen (animal/human hybrids) that most of the world shuns. The kingdom lost a war to Sana when he was a kid and he lost his parents in the war. On top of this, Bilibin, a neighboring kingdom, refused to help during the war and it wasn't till years later when Volechek became king of Belinsk that he defeated Sana and gained independence. Fast forward to the present day, Volecheck helps Blados and Chalis activate the Lunar Tower after he was told by them that it would help his kingdom rise up again and cease the attacks on his kingdom. Instead, it bathes most of the world in darkness and has shadow monsters running around killing people. He tries to sacrifice himself by trying to stop the source of the problem by himself while telling his sister, Sveta, to stay behind and keep the royal bloodline strong. At the end of the game, he comes back as a huge werewolf infused with Dark Pysnergy and can barely contain himself. Sveta recognizes him but is forced to fight him and against Chalis and Blados, and then once more when they are fused into him. After beating them for good, Chalis and Blados tells Sveta that even if they activate the cannon to destroy the darkness, the natural light of the world would eventually kill Volechek since he has so much dark energy in him. Wanting to save his brother and the world, Sveta goes to activate the cannon herself, but Volechek knocks her off and does the deed himself, knowing that the intense light bathing the weapon would kill him quickly. He simply says goodybe to Sveta before dying.
Seriously, Dark Dawn is full of this sort of thing. The deaths start piling up right after the Grave Eclipse. You can go through towns that aren't protected and look at the corpses of random townspeople who had nothing to do with any of this. And you can read their last thoughts. What the hell, Camelot?
Probably one of the best ones is the way you get the Crystallux summon. It involves failing to save a little girl and her grandfather and burying them both.
The dream version of Border Town. It's a happy, prosperous place where humans and beastmen are able to overcome Fantastic Racism and live together as a harmonious community. Compare it to the real Border Town, where half the town is cut off from the other due to an impending war of expansion, the buildings are falling apart, and the people are struggling just to get by. The only bright spot is that you learn that a child who happened to be on the wrong side of the town from his parents when the whole mess went down is likely being taken care of.
Oh yeah, speaking of Bilibin? Look at this little block above. Now look back at Volechek's handling of the war with Sana and its aftermath. With the Grave Eclipse having passed, the beastmen wil have to go back to worrying about Bilibin sooner or later. What happens next is on Bilibin's hands; the border could open peacably with new negotiations, and that dream would become reality. Alternately, the gate could open by force with Bilibin troops pouring through to test the new queen's might; such would prove that the successors to the McCoys are effectively void of a human spirit.
Still the McCoys, actually. Every so often you run across an NPC complaining about them, especially about the Lady.
Of course, this is all assuming that after the Grave Eclipse, Bilibin even exists anymore...
Obaba's plight is pretty tragic. By the time you meet her in Dark Dawn she has outlived her son and her grandson.