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.
Anthology II has a PMV sequence with clips of Rarity set to "Diamond In the Rough". Fast forward to 2014, and Rarity would refer to the Diamond Dogs as "diamonds in the rough" in the "Player Piano" Rainbow Rocks short.
Nightmare Fuel: "Stephen King's Equestria Girls" in Anthology III. Watch it here, but if you don't want to, it involves Human Twilight and Fluttershy standing around with a low-pitched horror chord in the background. Then, an arm comes out of Twilight's mouth, sucks Fluttershy's head until she turns grey, and the rest of her body falls off.
In Ponies The Anthology II there's a segment of the Time Machine from 2002 where Hartdegen arrives in 2037 and gets arrested for safety purposes. A little bit scary right there, until he looks up in the sky and sees the broken moon descending down on Earth, but Nightmare Moon is flying through the sky, laughing...