Cupcakes/WMG

In the Cupcakes-verse, Windigos corrupted Pinkie and caused her to become a cannibal and start the whole cupcakes thing.
Apparently, the Windigos were named after evil spirits that possessed people and turned them into cannibals. Perhaps the Windigos possessed Pinkie into doing it and they are the ones who make the rules?
 * Great, now I have this mental image of Pinkie Pie as a servant of Ithaqua, seeking to restore the Great Old Ones to mastery over Equestria. Ia, ia, Discord fthagn...

Pinkie Pie is the grim reaper for ponies
Well, this world runs on having ponies doing work that our planet comes naturally to us. So, why wouldn't there be a pony running the life cycles of each pony town/species.

Apple Bloom? well, eventually, the reaper's time will come too. Apple bloom is somepony she saw as a successor to her work.

The story was actually written by Discord simply to Troll the bronies
Why? Because being locked in stone is boring. And besides, that's just how he rolls.

This was an actual episode.
Kind of. They did animate it, get it into full color, and get all the voice recordings. It wasn't meant to be released, for obvious reasons, it was just to have fun. However, one day, in some foreign country were the show is popular, it accidentally got broadcasted once. They stopped it from happening again, but not before scarring a lot of children. Someone in the US found out, and proceeded to write a story about it and publish it to the Internet.
 * Alternatively, Cupcakes is a MLP episode from a parallel universe where the series was created by the Tsalal.

If Rainbow Dash hadn't shown up when she did in Party of One, this fic would have happened.
You can't tell me that if it took them 5 minutes to convince her to never invite the other ponies to a party again, that given more time the Companion Cube squad wouldn't have convinced her of this. What makes this truly frightening? Cupcakes was written before Party of One aired.
 * Except in the fanfic she'd already killed Gilda after the episode she appeared in. So if we're applying the show's canon, she's been killing long before Party of One (unless you believe in the theory that the episodes are out of chronological order).

Pinkie Pie is related to BEN somehow.
Think about; both of them take captive of an innocent bystander for absolutely NO reason and proceed to torture them, both are childish, and both are working for someone they know/are related to.

BEN: Majora Pinkie: Apple Bloom Both of whom are trying to kill everyone they can. Thoughts?

This Pinkie Pie is a Changeling
Or otherwise not actually real Pinkie.
 * can also apply.
 * Alternately, this Pinkie Pie is the real Pinkie and Rainbow is the fake. If the fanon that the changelings share a hive mind is true, Pinkie's a magnificent bitch going after evil changelings while posing as a serial killer so she doesn't tip them off. Although she may be Becoming the Mask.

Cupcakes happened because of Rainbow Factory (i.e. they're in the same universe)
Rainbow Dash's number wasn't originally that low,. However, after the events of Rainbow Factory, Pinkie didn't know who to kill because Dash screwed up the list, so she settled with killing Dash.
 * This would make the fanfiction a lot more bearable.