One by one, Twilight and her friends must come to terms with the consequences of being the Elements of Harmony.

These stories take place in the intervening time between Season One and Season Two,
with the exception of Ditzy Doo: Muffins, which takes place early in Season One.

The series continues in the sequel, Secrets and Lies.

Pony Psychology has a TV Tropes Page.

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.

It's been a few weeks since Luna's returned from the moon, and all is not well. She's become more introverted than ever, rarely leaving her room and obsessing over work. Celestia hopes that studying Twilight Sparkle's Friendship Reports will at least help her get out of her shell, though an unusually talkative servant may just help in that regard...and is anypony else getting strange feelings from that statue out in the gardens?

As of May 4th, now featured on Equestria Daily. *Squee*

Celestia and Luna were born as unassuming foals in troubled times. But already marked for greatness, the simple earth ponies stand to face a world set against them, full of danger, fear, and sadness. A world they will change forever.

A sweeping epic taking place before Equestria was made, where Celestia and Luna must rise from normal foals to become the Princesses we know them as, beset from all sides by monsters, other ponies, and even the forces that govern nature. Their tale is as tragic as it is triumphant.

Currently on hiatus. For more info, go here.

(Cover and internal art by Madmax)
(Editing credit predominantly Lightside Luc)

This story is a sequel to My Little Alicorn

After the events of "My Little Alicorn," everything seemed to be back to normal...except for one pony. Prince Blueblood is now trapped as a colt, his title, possessions and birthright stripped for his crimes. Before Princess Celestia will return him to normal, however, he must prove himself by attending Magic Kindergarten. Even worse, his current situation has attracted the vengeful gaze of two ponies he has offended in the past: the Captain of the Royal Guard and the Moon Princess.

Will Blueblood rise above his past self and emerge a better pony? Or will he sink back into his old depravity, and be stuck a colt for the long term?

Note: This is a sequel to "My Little Alicorn," so you might want to check that out first.

From the Canterlot Vaults comes newly found and remastered episodes of everypony's favorite dynamic duo. Experience the action all over again as Luna's forces close in on the helpless citizens of Metropony with only Harpflank and Sweets standing in Her way! Watch as these classic stories come to you in all their Rainbow-Ray glory!

Filling in Season 1 episodes with permission from Arcainum.

What if Twilight and Trixie were both zeppelins who were in love? At last this age-old question has been answered!

Night and day. Fire and ice. Creation and destruction. Everything has an opposite, and Chaos is no exception. Princess Celestia tells Twilight the true history of Discord's rise, the Alicorns' fall, and the creation of the Elements of Harmony.

She tells her student the story of Order and Chaos.

The bustling city of Metropony is under siege by Luna and her villainous assistant Trixie's army of deadly Lunatrons! Can Lyra and Bon Bon's crimefighting prowess and vast supply of heavy munitions keep the city safe for yet another week? Find out in this exciting episode of... HARPFLANK AND SWEETS. Warning: Not suitable for under-5s or those of an unawesome disposition.

- Now with added side-story, by supersheep64! - Harpflank and Sweets: The Lost Episodes
- Now with more added side-story, by RTStephens! - Haprflank and Sweets: Season 1
- Now with further more added parody, by Cold in Gardez! - Harpflank and Sweets: A Very Special Episode
- Now with extra further more added parody monstrosity, by Blueshift! - Sweetflank and Harps
- Now with extra TVTropes!
- Featured on EqD, rated 6-Star, for what it's worth!
- Exclamation marks!

When Metropony city falls under attack, who is there to save her?

That's right! Harpflank and Sweets are back, in the never-before seen lost episodes from their iconic first season!

The not-lost episodes: http://www.fimfiction.net/story/7621/Harpflank-and-Sweets