My full list of recommended stories can be found here.

Stories I have called out in particular:

Short stories:

A Lot To Think About - In the aftermath of the ruined wedding of Shining Armor and Princess Cadance, Celestia and several others maintain a vigil at Canterlot General Hospital. AU.

A Million Things To Do - Pinkie Pie comes to Rainbow Dash with shocking news; the world is going to end, and they have a million things to do before it does. Although Rainbow Dash agrees to play along, she obviously doesn't take her seriously... but as the day goes by, the true meaning of Pinkie's warning becomes clear.

Who We Are - Twilight receives a letter informing her that one of her friends is - and always has been - a changeling. But who, and what does that mean for their friendship, when they cannot even tell their best friend what they are?

Variables - Spike talks to the statue of Discord, shortly after he was turned back to stone.

The Numbers Don't Lie - When the Cutie Mark Crusaders dig up an ancient magical artifact, they unleash a spell on the town that allows everypony to see a "lie meter" floating above each other's heads. While attempting to solve the mystery, Twilight Sparkle has to analyze the tenuous balance between friendship and honesty. She doesn't like what she finds.

Storm - A storm of epic proportions sweeps over Equestria, leaving the ponies of Ponyville to try to piece their lives back together.

Plucked from the Air - Lyra and Bonbon want a kid, but the adoption agencies are less than eager to hand a child over to fillyfoolers. Soarin gives them "another option". Clop with class.

Dance Til We're High - Twilight Sparkle, lonely as her friends all begin to find their special someones, goes to a masquerade ball with Rarity to meet new ponies, but wasn't expecting to dance with the pony of her dreams. But who is this handsome masked pony?

Mood Wings - Twilight learns about pegasus body language and goes around town ogling every pegasus for research purposes.

The Glass Blower - A pony fairy tale.

The Light in the Darkness - Pinkie Pie has a horrible nightmare about murdering all her friends; Rainbow Dash helps her deal with it.

Diamond in the Rough - Applejack gets drunk and lets Rarity know how she REALLY feels.

The Cough - In the darkness, somepony coughed.

Cumuliform and The Next Day - Rainbow Dash doesn't know what day it is. This bothers her greatly. She decides to go talk to Celestia about it. She doesn't know either.

Rainbow Dash Gets An Abortion - When Rainbow Dash wakes up with morning sickness a few weeks after a big party she is forced to make a hard decision.

Long Stories:

Tiny Wings - Scootaloo gets some flying lessons from Rainbow Dash. But lessons don't give you bigger wings.

Hard Reset - Twilight isn't having a very good day. An experimental spell blew up in her face, an army of changelings is attacking Canterlot, and she just died. Yet somehow, it looks like it's going to keep going downhill from here. Given the chance to correct what's gone wrong, Twilight swears she's going to fix all this even if it kills her. Which it will. Frequently.

Arrow 18 Mission Logs: Lone Ranger - Humanity has detected a star orbiting a planet and sends a ship to investigate. Science fiction meets Equestria.

Ongoing stories:

Hooves Holding Hearts - Lyra and Bonbon's trial and trevails in adopting a child.

Playing With My Heart - Octavia is in a coma, and Vinyl is waiting by her bedside until she wakes up.

Changes - Derpy dies, leaving her two children in the care of Rainbow Dash.

A Terrible Reason To Be Unhappy - Rarity loves Applejack. Applejack loves Rarity. But Rarity can't stand Applejack, so they break up. After all, love is a terrible reason to be unhappy, right? But will breaking up make them any happier?

Can be found on archive.org at https://web.archive.org/web/20150320115529/http://www.fimfiction.net/story/148361/a-terrible-reason-to-be-unhappy