These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Harsher in Hindsight: One episode of the actual show involves Pinkie Pie having a psychotic break and being in a room alone with Rainbow Dash. The fic became more disturbing thanks to that coincidence.
Naturally, this one ('Party of One') is relied on for the trailer.
"Green Isn't Your Color" becomes... unsettling after reading this fic. The creepy stalkerish thing is bad enough, but she also threatens Twilight Sparkle by taking a bite out of an apple. And shortly afterwards we're treated to a closeup shot of cupcakes. Brrrr.
Hype Backlash: Some people slept just fine after reading this fic.
Cupcakes itself predates a certain horse meat scandal.
It Was His Sled: The fact that this story was "Grimdark as Fuck" was intended to be a big twist originally. Seeing how this story has been mentioned all over the internet and the fact that it is labled as "Grimdark as Fuck" that twist has long since been spoiled.
Internet Backdraft: Just the simple mention of this fic in some parts of the fandom can cause enough bile to fill ten olympic-sized swimming pools. Bonus points if you say you like/dislike this fic for any reason.
Magnum Opus Dissonance: Of a sort. The author appreciates all the fanart, AU's, and general publicity, but would prefer some attention for his non-grimdark and more respectable works. Since his name is almost always associated with his infamous fanfic, it's not likely.
The mental imagery caused by the basic premise of the plot itself, the shocked/disgusted/horrified reactions to the fanfiction being spread around by fainthearted readers (or at least those who have heard of it but haven't read it yet due to fear of being scarred and traumatized for life) across the Internet and the various fan arts it gained had made the fanfiction appear much worse than it actually is.
Memetic Psychopath: This fic is single handedly responsible for turning Pinkie Pie into one.
Ron the Death Eater: Take a character who is not only a hero, but a nice character overall, though somewhat bubbly, and make her the extreme opposite, though still technically who she is, just insane, and bam, you've got Pinkie in this fic.