Rainbow Dash has been dating Pinkie Pie for nearly a month and, in spite of Pinkie’s objections, is keeping the affair a secret from the rest of their friends. Deciding she's had enough, Pinkie Pie throws a party announcing their relationship.

When Rarity’s friends discover that she has been seeing an escort, they decide to investigate and find out why. What they discover is more shocking than any of them could have imagined.

An alternate and significantly better version of this story can be found here.

Who is Scootaloo? Everypony knows about her present, but when it comes to her past there are as many different answers as there are questions.

Is she the love child of two star-crossed lovers? The last hope for the future? The child of a broken home? A mysterious figure fighting a war no pony knows about? Or is it something else entirely? Is she even a pony at all?

Twilight Sparkle decides to ask everypony in Ponyville and find out about Scootaloo...and the stories, rumors and gossip she gets will leave her wondering how the truth can ever compete with fiction.

My thanks to Page Turner for the new story cover!

Now has its own TVTropes Page!
http://tvtropes.org/pmwiki/pmwiki.php/FanFic/TheManySecretOriginsOfScootaloo

And has a featured page in the Non-Canon My Little Pony Funny Page!
http://tvtropes.org/pmwiki/pmwiki.php/Funny/TheManySecretOriginsOfScootaloo

Thanks to all my readers and fans for all the support and help I have gotten! I am truly touched.

Octavia is a high-class pony. Fine alcohol is her wont, and uncouthness her intense chagrin. Such is her surprise to find herself lumbered with an insufferable oaf of a DJ pony. However, sometimes these situations work themselves into a satisfactory ultimatum all the same.

When Octavia and Vinyl Scratch decide to combine their respective musical styles into a new genre that will celebrate not only their talent, but also their unique bond, they feel confident that they're the pioneers of the new age. So when the two find their music challenged by another pair of musicians, they set out to make sure that theirs is the best. However, the rival two aren't bad artists themselves, not to mention they’re certainly not… of the same persuasion as Vinyl and Tavi. In the snow-wrapped streets of Manehattan, can they risk exposing their new found -and still taboo- relationship, or will they be doomed to second place?

Incredible cover art by JackiePhantom13! DA: http://jackiephantom13.deviantart.com/

EQD!!
Link: http://www.equestriadaily.com/2012/04/story-mixing-relationships.html

Luna has had enough of Celestia's games, and has found the perfect means of revenge. Using a long-forbidden spell, she transforms her sister into little more than a small filly, all so she could pull the greatest prank ever. Unfortunately, she soon learns that before you fool around with dangerous magic, you really need to read the fine print...

A sequel can be found here.

All Princess Luna wanted was to wake up and enjoy her night, but after getting pranked one too many times by Philomena she is determined to get revenge. Can the palace withstand a prank war between these two?

Now on Equestria Daily

Applejack's got a secret she'd kept hidden for many years. Nopony would ever have guessed what she and Twilight were up to in the library late at night, once Spike had gone to sleep. That is, until a jealous Rainbow Dash decided it was her business to find out just what in the hay was going on.

The following transcripts are of a journal found in Ponyville on April 16th of this year. The last recorded contact with the town had been 3 days prior, on the 13th, when a team under orders from Princess Celestia was sent to look into several missing pony reports in the area. When another group of investigators were sent on the 16th, the town was found deserted. The journal’s owner is believed to be the princess’s personal student, Twilight Sparkle. None of the town’s inhabitants have been located in the weeks since.

Readings:
Nimbus Productions
Scribbler Productions

I highly recommend both of them.

A print version of all the stories in this series can be found here. (There is currently a printing error I am working to correct. This will be available again soon.)