Please don't list this on a work's page as a trope. Examples can go on the work's YMMV tab.
Nightmare Fuel: Touhou
Don't touch the flowers.
A good amount of fanworks tend to portray Gensokyo as a nightmarish place, despite the fact that all the demons and monsters are cute girls more interested in games and parties than anything else. The "Test in Touhou" videos are primeexamples of this.
Looking carefully at Konngara, what appears to be blood is dripping from the base of her "horn". It's likely a spike driven through her head.
It is somewhat common for fans to depict Yuuka and Flandre as destructive, maniacal monsters. While others go in the opposite direction with "youkai moe~" and Cheerful Child depictions respectively, it says something about their status when any image of them giving a hug on Danbooru is met with many comments along the lines of "OH GOD NO!!". It Gets Worse when you realize that the description "youkai moe~" is a pun on Yuuka being a flower youkai ("moe~" means "budding") ... her real personality is evident from her route in Phantasmagoria Of Flower View and it is not pleasant.
One of Yuuka's lines in her scenario in Mystic Square is "Genocide is just another game." Whether she is actually serious or merely trolling is up to debate.
The inside of Yukari's gaps contain countless unblinking eyes and arms trying to claw their way out.
Pretty much everything about Highly Responsive to Prayers was highly unsettling. Especially Sariel and Konngara. While Sariel looks like a beautiful angel, she's actually an angel of death. The background goes through changes throughout the battle of her first form, and in one of them you can see a bunch of hands rising out of the ground. You can't even clearly make out her second form. You can see the outline of her body, but the rest is a giant void. To further drive the point home, there is no dialogue, and there just is ''something'' about the dark atmosphere in the entire game.
There's actually a bit of Fridge Horror regarding Remilia and Flandre. If you read through Remilia's profile, it states that Remilia can't create more vampires because she doesn't have the appetite to drain all of a person's blood, confirming that vampires need to feed on a victim to turn them. Combine this with the fact that Remilia is stated to appear as a child, and Flandre is a whole five years younger than her. Some vampire out there nommed on two little girls who were probably somewhere around 5-10 years old!
It's said that the reason Reisen's eyes appear red is because the mind of the person observing them is receding, fast.
Medicine Melancholy, full stop. Sure, she's just a sentient doll, but her genocidal ramblings, her thoughts of pure hatred against humans, and how she has no qualms in testing the effects of her dangerous poison on them or killing whoever steps into her territory drive her straight into this category.
The Scarlet Devil Mansion. According to game manuals, it's much larger on the inside, monochrome, and very dark. It would be very easy for someone to get lost. Also, if you fell down a hole (which apparently exist in there, according to manuals), no one will hear you, and you will most likely be stuck there until you die of lack of water/food.
Kisume has been revealed to chop off heads and hide them in her bucket, and the head you see might not be her own. But the real creepy part is that she seems completly unaware of her actions.
Beware of traversing The Dark Side of Nico Nico Douga. They have Seinen depictions of Touhou itself, most of which contain the R-18 tag. The tag name for Touhou, appropriately enough, on Google Translate roughly means "Gensokyo is a scary place".
The fan-made music PV "Josei no Qualia ~ Subterranean Rose", created by Innocent Key, is a classic example of such a Seinen depiction. Sure, we love Koishi's alternate outfit that she wears on there, but the fact that she puts Marisa on a crucifix, rips off her clothes through Clothing Damage, and sometimes gets a downright insane look on her face when she attacks, not to mention giving off a Slasher Smile, is pretty freaky.