This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / My Little Pony G3
Some of the Uncanny Valley moments. The two Newborn Cuties shorts are the worst, since their mouths almost never move.
A Very Minty Christmas has Minty and Thistle Whistle almost falling to their deaths when the hot air balloon popped over a canyon.
In The Princess Promenade, Spike cheerfully tells Wysteria goodbye after he thinks she doesn't want to be a princess and begins to fall asleep; Wysteria says if he goes to sleep he'll nap for another thousand years—meaning she wouldn't live nearly long enough to see him wake up.
In The Runaway Rainbow, the loss of rainbows may not seem that big a deal—until you remember Sweetberry said rainbowberries grow only after the first rainbow of the season. Rarity unknowingly put Ponyville's food supply in jeopardy.
It's worse than that: the world would have lost all color. On top of that, if the Newborn Cuties are taken into account and we assume the bizarre creation of Sweetie Belle (she fell from the sky where two rainbows crossed) goes for all ponies, no more rainbows is nothing less than an extinction-level event. And just think - every season this must be done again. If they screw it up once, that generation is the world's last.
This profile◊ of Kimono's was written before G3 Unicorns were made, but it doesn't dispel the theories that something happened to separate the three Pony races.
What Wysteria goes through for being a princess, and the implications that before her, all princesses were like this.
The Runaway Rainbow has the ponies nearly going over a waterfall.