This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Rule of Rose
A bright red crayon, just for you.
The whole game fits this trope once the player fully understands what’s going on.
“The Unlucky Clover Field” chapter shows Martha being beaten and dragged up a flight of stairs by some imps. Towards the end of the chapter, we see Martha’s dead body being stuffed under a bed, her eyes still open and her foot dangling above her head.
Jennifer finds her in the chapter-after-next chapter, tied-up, with a bloody bag over her head, and a newspaper around her waist. Her feet are still moving.
The very first imp that you encounter. At first, you can see it curled up on the ground crying, thinking it's a child, until it turns around.
"The Mermaid Princess"
It's made even worse once the player puts all the clues together. Clara is clearly being molested by Hoffman, who can be seen stroking her in bed right before the boss battle. Then you notice the stitching on her abdomen, and one of her attacks is to spew vomit on you.
"It's into the Onion Bag for her." Cue horrible, horrible children doing something utterly repulsive to Jennifer.
The children's bag masks.
Boss Hoffman, especially in a scene earlier in the chapter where you can have Jennifer peer into the locked sick bay and see imps controlling him.
Its even worse when the player connects him to Sir Peter and relates it to the storybook at the beginning of the chapter.
Especially considering that Hoffman is a pedophile. Brings new meaning to the phrase, “holding it in”.
Even more creepy when you find a hat that looks exactly like Sir Peter's in Hoffman's closet.
Jennifer lost her parents in the airship crash, was then held captive by Gregory and dressed up like his dead son, probably spent some time in a hospital, came to an orphanage filled with sadistic children, and later witnessed their deaths at the hands of Gregory. What an unlucky girl indeed.
The first time you see a pig imp.
To elaborate, it walks out of the port livestock room and squeals at you. As its mouth opens, you see an ordinary imp's face inside its mouth.
Wendy seems to be the only person who really likes Jennifer. Then you realize what she’s capable of.
Even Amanda seems to be okay with Jennifer until she passes her in ranking. Hell hath no fury like an obese British girl scorned.
The opening to the game sums up everything. If anything in that clip disturbs you, don’t bother starting a new game. It only gets worse.
When you find out what happened to Brown.
The entire "Rag Princess Sews" chapter. First of all, the music in the level, unlike the other chapters that used pianos and strings in the background, is replaced with a Silent Hill-esque industrial sound. Second, being in the dark in such a huge place is not pretty. Third, having to chase "Joshua" in such long, dark hallways and having to battle several endurance rounds with the toughest enemy type is one of the scariest moments in the game.
Everything that happened to poor, poor Gregory. A prepubescent girl takes advantage of his psychosis and turns him into a serial killer.
The creepy man (who turns out to be Gregory) that keeps showing up with hand drawn picture books calling Jennifer "Joshua."
Look at it from the Rat's perspective: the first time we see it, it is bound to a stick and pushed into some poor girls face. The next time we see it, it must have been dead for days, if not weeks. And if you look closely, it is bound in the exact same way as before. Nobody ever bothered to free or probably even feed that poor animal.
Animal abuse is a theme in general. While it is questionable about any pigs or goats ever having even existed, there are hints on Diana not properly caring for the aquarium, leading to dead fish. The first required gift is a butterfly, leading to the chapter being filled with the children hunting and killing them. Wendy was responsible for the bunnies , but the Epilogue chapter leads to Jennifer saying that she stopped doing that and we not only find empty cages at the beginning, but there is a whole chapter dedicated to a dead rabbit. And then of course what happened to Brown...
"A bright red crayon just for you. A bright red crayon just for you. A bright red crayon just for you. A bright red crayon just for you. A bright red crayon just for you. A bright red crayon just for you. A bright red crayon just for you. A bright red crayon just for you. A bright red crayon just for you."
There's something deeply unsettling about reading the catalog in Sanity Slippage that is Amanda's diary.
There is a scene that is very easily missed in the opening. Remember the moment where Diana, Meg and Eleanor are shown hammering the coffin? Well right before that there is a moment showing them hammering a bag in the attic. By the end of the game we know that Wendy and the rest of the aristocrats killed Brown. We're never told how they do this in the game itself and we are lead to assume that, because of the cut scene that's shows the imps (the darkest form the rest of the orphans take in Jennifer's head) sweeping a non-bagged Brown and the fact that Brown had previously been seen by both Jennifer and player as a full grown animal (that would have been hard to put in a bag while still living) up to that point in the game, Brown was put into the bag after his killing. However we are shown during the true ending that Brown was actually a puppy when the events took place. (Similarly how Jennifer was actually a young girl. That brief moment in the opening then gains some meaning. This means, under the orders of Wendy, Diana Meg and Eleanor kidnapped a defenseless puppy, shoved it in a bag, took it to the attic, and hit it to death with hammers. The fact that three girls can be fooled into killing a puppy is both incredibly disturbing and utterly heart wrenching at the same time.
At one point, Jennifer will note that first Martha, then Hoffmann and Clara disappeared and the children were left to their own devices. While it is questionable how much is real and how much is made-up, it is heavily implied that Martha got murdered by the children, Hoffmann hung himself in the staircase and Clara killed herself as well. While Martha is very obvious in it's implications, Hoffmann is shown by the Sir Peter story of the rabbit hanging himself at the end as well as the shadow of an adult hanging being visible in The Funeral. While Clara isn't shown directly, she is mentioned in the same sentence with the others. And later in the rose garden, the player can find that Gregory had been digging three graves...