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 and her five friends are transported during a botched spell, across dimensions to... Ponyville, Equestria? But not the same one that they knew. Sitting on a bench is Harpsy and Babar. The Doctoress avoids apples from an aspiring Applebuck. And in a library across town, six stallions join their forces as they try to decipher the appearance of filly look-alikes of themselves around Ponyville!

Pinkie Pie is being tormented by horrific nightmares. Unable to deal with it by herself anymore she seeks out Twilight's help, but will it have been the best decision when she finds herself alone in an abandoned, fog filled Ponyville?

Sequel: http://www.fimfiction.net/story/4676/Too-Shy-for-a-Rainbow

There have been a LOT of high-quality readings of Silent Ponyville, but this one is my personal favorite:
https://www.youtube.com/playlist?list=PLGh01rbB4o3xoSV7a6Omc-UJROXHRZ1Hv

Twilight's curiosity pushes her to go where no bookworm has gone before: on dates. Dates with lots of unfamiliar (and not so unfamiliar) mares. It goes about as well as you'd expect.

A parody of dating websites in general, named after eHarmony.

Twilight Sparkle is summoned to settle a legal matter involving The Great and Powerful Trixie... What in Equestria did she do now?

When Rarity is overwhelmed with making designs for an agriculture exhibition, she turns to Applejack for advice. But when she gives Applejack a hair style treatment in return, the apple farmer lets her accent slip from southern drawl to sophisticated Manehattenite. The result? More fancy parties than you can shake a candy apple at!

Luna discovers something hidden from Celestia for twenty years, now, with emotions running high, she enlists the help of the Mane 6... but what seemed to be a single mystery, soon reveals a darker and much more complicated plot that will soon decide the fate of Equestria.

Check out the Empty Room TV Tropes Page (Warning: Spoilers!)

Revised chapters edits and proofing (with many thanks) by: lammy, Trevor, Nick Nack, Fifth Alicorn

New! Part 3: After Twilight notices Applejack becoming increasingly obsessed with the game, she tasks Pinkie Pie (of all ponies) to keep an eye on her. The two head out into Ponyville in search of adventure and the perfect game.

Part 1: Twilight has finally convinced Applejack to join her other friends in Spike's weekly D&D game. However, will she be able to figure out the rules before they all drive Spike crazy?

Part 2: Applebloom, Scootaloo, and Sweetie Belle have stumbled across Twilight's D&D books, and convinced her to take up the dice once more. But will anypony meet their high standards to be their Dungeon Master? More importantly, what will happen when you-know-who finds out?