A face leaned around the door; it was wearing a bleached white mask, the eyes crossed off with frantic scribbles of black and twin tears of red depicted rolling down the face. The mouth was a manic grin, twisted by a level of instability Applejack had only seen in the mentally unstable.

I re-read this paragraph a couple of times. At first I thought it was You-Know-Who, but I realized that couldn't be right.
After going over it in my head a few times, it finally clicked in place:

Masky:
vignette3.wikia.nocookie.net/theslenderman/images/6/65/Tims-Ninth-Appearance.png/revision/latest?cb=20120929234013
I was originally reluctant to suggest that this was inspired by Marble Hornets, but now I have no doubt. Not that it's a bad thing, far from it. If anything, that just makes it more frightening.!

7273410
Oh, that's not entirely true. Slenderman has numerous proxies, depending on what version of him you're looking at. For instance, another mask-wearing proxy is Kate the Chaser from The Arrival.

Many people believe it's a side-effect of overexposure to Slenderman's presence or direct contact with the entity in question.

-Inkheart

7273707
Funnily enough, Kate and The Observer were two other examples I had as part of my original comment, before deciding on just Masky.
Now I'm left wondering who it is. None of the ponies that have vanished so far had yellow manes. In fact, the only pony in Ponyville with a yellow mane I can think of is Derpy. And the CMC didn't record her on their camera.

Although Daisy and Lily do have manes that are yellow-ish in color...
Hmmm...

7274115
Nope. Daisy's mane is lime.

pre13.deviantart.net/114a/th/pre/f/2013/150/4/1/vector___daisy_by_ready2fail-d678o35.png

And those are only the proxies from video games and vlogs; I'm not even counting the ones from regular Blogs.

-Inkheart

Please continue this awesome story, I am eager to read more.