This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Breath of Fire II
The FIRST thing that happens in the game. Kind of unfair really.
Pray to God! Praise God!
Coming back to your hometown with no one having any recollection of you or your family having lived there is pretty horrifying.
In the Grand Church, the mob amassed. You have a gem that reflects a person's feelings toward you. As they are baying for your blood, the gem turns PITCH BLACK.
When the people kidnapped by the church are imprisoned in Bando, they're left there to go completely insane, until they begin to pray to St. Eva for salvation and freedom. In the process, this tears their souls apart, leading to the terrifying, puppetlike husks seen in Evrai.
Speaking of which, those folks in Evrai? When you first meet them, they seem rather pleasant, happy-go-lucky sorts. They speak of how happy and content they are, and the reflecting gem shows them all with peaceful colors. Try to leave, though, and you get trapped inside the town... Where the townsfolk are suddenly muttering and babbling and laughing incoherently, showing only faint, tormented vestiges of any awareness whatsoever, and the gems shows dark, cold colors for all of them.
And finally, once you defeat the Load-Bearing Boss in Evrai and make your escape as the city and the church crumble and explode, St. Eva's victims all sit in the pews... Simply chanting/praying mindlessly, over and over again, as they're all about to die (if they weren't already dead in the first place). It's hard to say whether they're even aware of anything anymore at this point.
Shupkay's fate in Highfort. She unearths a mechanism that pops up a few times throughout the game, a device created to use a person's life energy as fuel for whatever purpose it was designed for. In this case, she intended to utilize Highfort itself as a massive floating weapon to wage war, and use Highfort's princess, Elforan (Sten's love interest), as the energy source. She also planned to kill Sten in front of Elforan to further amplify her energy. Instead, Shupkay ends up inhabiting the machine herself... Which, due to malfunctions, causes the machine to pump energy INTO her body. She explodes. Granted, she was an Asshole Victim, but still: Ouch.
Inside the Wise Tree's mind, you can find a man named Barose and recruit him for your town. He'll offer to teach the front character in your lineup magic if they have no AP left. What makes him creepy is that the Dragon's Tear is permanently locked on dark red (animosity) with him. For some reason, this guy hates you. He has no impact on the game at all.