Rainbow Factory is a creepy pasta, first created by Wooden Toaster with the song "Rainbow Factory", and then made in a fanfic by AuroraDawn. The story tells us about how Rainbows are really made (since we watched how they were put on the sky in one of the episodes). Basically, the colors of the rainbow are made from ponies (specially pegasus who failed the fly test), cracking their bones and throwing them into a machine that takes their color by (I guess) crushing them. That's, at least, the version of AuroraDawn.
Some other artists have made their own version, from stabbing the ponies with a huge needle to extract the color to cutting them.
It's a very dark creepypasta, and usually involves Rainbow Dash as the owner of the Factory where this happens (original idea by AuroraDawn).
Lol...cupcakes...another creepy story. First of all, video (don't watch it if you are really young or scared of....blood): [link]
Cupcakes is a story about Pinkie Pie doing cupcakes with a special ingredient, a secret one that no one knows. She picks numbers and the one that comes out, is invited to her home to make cupcakes with her.
Rainbow Dash is the one invited this time, and she goes. Pinkie Pie then starts to torture her (Dash is usually tied to a medic table or something like that), cutting her wings, cutting her cutie mark (it is implied that Pinkie collects cutie marks, wings and horns for her dress), electrocuting her with electricity, some other things and finally, cutting her stomach and taking her intestines and all under the ribcage, and finally killing her (I won't tell you how she kills her, is really digusting).
Pinkie then makes her cupcakes with Dash's entrails, and stuffs Dash to keep her.