This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Professor Layton vs. Ace Attorney
As mentioned on the main page, the Ascended Fridge Horror of true culprits being executed in Ace Attorney shows up as early as chapter two, when two young girls are executed - one of whom was (presumably) innocent. Both are locked into an Iron Maiden-esque cage, then slowly lowered into a pit of fire. Both scenes are fully animated and voice-acted, so you can hear their terrified begging until the cage finally cuts them off.
Once you start to suspect them, the real culprit of the second case has a sudden shift from kind flower seller to complete and total psychopath, complete with Nightmare Face and Slasher Smile. Yes, we've seen creepy "transformations" in Ace Attorney before, but this is the first one to be fully voiced, so you're hearing the crazy as well as seeing it. In particular, their increasingly fast speech as they frantically explain why you have no evidence against them, ending with a completely calm "You. Lose.", complete with Slasher Smile.
Maya and Layton are both as good as dead for a portion of the game! Layton's solid gold body is displayed behind the defender's bench during the second witch trial, and Maya is dropped into the pit of fire in the same way as the other witches.
Layton himself. When he does that desk slam thing, he actually can be pretty scary, and it's even worse when he's on the Prosecution's side. Holy yikes.
The Legendary Fire that destroyed Labryinthia and left no survivors is, in itself, already a little dark for a Professor Layton story. What pushes it into pure nightmare territory is that it was indirectly caused bytwo young children playing where they weren't supposed to be. They were then forced to watch the town burn around them. "Traumatized" doesn't quite cover their reaction.
To top it off, the reason that the Legendary Fire killed so many as it did is because of the Bell of Ruin which renders people unconscious when they hear it owing to a type of poison in the water causing people to fall unconscious whenever they hear anything made of pure silver. And they were unconscious at this point. Imagine being burned alive and you physically cannot do anything to stop yourself from suffering that horrible death.
And to cover it up? The Storyteller, really a terrified father, has to use his money and hypnotism to make everyone in Labyrinthia believe that they were villagers their whole life. Why? Because it was the girls' therapy. Imagine having to play a role for who knows how long so that two kids, innocent or not, could heal. And not to mention that "witches" are being cast into fire for their sake, for causing the whole fire in the first place all because no one could keep an eye on them!
The Burn the Witch! mentality of courtroom sequences. When witnesses lie in the witch trials they often have no idea whether or not the accused is actually guilty - instead, they just want to see someone burn. Even the gallery views Phoenix as a monster for trying to defend his client and will actively cheer Barnham on whenever Phoenix does something right. It gets especially unsettling in case three when Luke takes the stand. Not only is he a child, he's fully aware that his testimony may get Maya killed. And he doesn't care.
It gets even worse when you realize that, other than the fact that magic wasn't actually used, this is more or less how Real Life witch trials were carried out: no evidence, no logic, no reason, just a room full of bloodthirsty townsfolk looking for any reason at all to watch someone burn. Seeing them played out before your eyes really gives you a new perspective on how severely messed up society was back in those days.
How did the massive project of Labyrinthia get its funding? From the UK government. Why did they fund it? Because they wanted to see if it was possible to brainwash large numbers of people for sustained amounts of time. Yes, that's reassuring. No way that could be used against the general populace.
Towards the end of the game, Layton and Luke have to take on a few puzzles that are heavily implied to have life-threatening consequences should you fail them. Of course, you don't actually see anything happen, you just get a "try again" message and the puzzle restarts, but it's still pretty unnerving. One involves having to unscrable a set of tiles, but you only have a limited number of moves... because evey move you make, a giant, creepy-looking statue takes one step towards you. Later, the Stroyteller outright attempts to kill Layton with an army of robot knights (as he writes about Layton's "tragic end"), and you have to fight them off in a puzzle. Just be thankful this isn't a Sierra adventure game...