A letter from Celestia interrupts one of Pinkie's parties with disturbing news. Now friendships will be pushed to the limit as Twilight struggles to uncover which of her friends is not who, or even what, she appears to be.

(While not a romance, this does contain a shipped pair)

in Russian

When they first moved to Ponyville, Fluttershy moved into an ornate cloud house, and Rainbow Dash moved into an animal infested cottage. As they settle into new lives and meet new ponies, they quickly discover that this isn't going to work at all.

"Like two peas in a pod we did everything together!" sang Twilight in the season finale. But what if she was letting on more than everyone else knew? What if Twilight really was a pea?

Twilight Sparkle and her fellow Elements of Harmony have faced down supernatural foes of the highest order, but sometimes the deadliest danger can come from places one would least expect. As Twilight is forced to bear a devastating secret, her efforts to keep the Elements together may well tear them all apart.
The plotline of the thrilling Pony Psychology Series continues with an exploration of deception, despair and Discord.
This series takes place between Season Two and Season Three.
Secrets and Lies shares the Pony Psychology Series TVTropes page.

Distance can drive us apart. It can also bring us closer together.

After all is said and done, and the ponies have gone their separate ways, the only way they have to keep in touch is through letters.

Original Equestria Daily post is here
Russian translation
Chinese translation
Polish translation
Spanish translation

Now with music and audiobook

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.)

Some secrets need to be kept, and others need to be set free; but sometimes, not even the Element of Honesty can tell the difference. How do you tell your family the truth about something that you can't even admit to yourself? When Applejack begins to realize that she may have feelings for a friend, she needs to find the courage to accept who she really is before she can truly be happy.

It's been five years since she first met them, and most of Twilight Sparkle's friends have found love, leaving her feeling left out and unwanted. The Winter's Eve Ball promises a magical night of mystique and romantic wonder, but will Twilight's romantic notions get the best of her? Based on the song by the Fireman.

Originally published on Equestria Daily November 29, 2011.

Be sure to check out the song by Baron Thyrai!

Twilight Sparkle is a gifted student and scholar. When she attempts to harness her creative side by writing a science-themed sensual romance novel, however, things rapidly get out of hoof. Can her friends stage an intervention before she humiliates herself (and them) at a prestigious literature recital?

No. No, they cannot.

What would you do, if you met a pony who was at once your brother, and yet not? Applebuck wishes to reunite with his 'Cousin JayJay', and braves the dimensional divide to reach his goal. But being a small foal, how will he deal with a world in which everything is flipped? His friends, his family, and even... himself?