This story is a sequel to Dresden Gets Schooled

Harry Blackstone Copperfield Dresden's life has been even stranger than usual ever since he first got involved with Equestria. However, after his last adventure sent him to some strange high school dimension, things have finally settled down into something approaching normalcy. Or at least as normal as Harry's life ever gets. His new apprentice Sunset Shimmer is proving to be quite a handful, but Harry has experience with handling headstrong young women.

However, things take a turn for the worse when he learns that a new threat from Equestria has made its way to Earth. And naturally it's up to him to stop the Sirens before they rock the world's foundations.

Cover art by Pon3Splash

This story is a sequel to The Rainbow's Surprise

On the day of Fluttershy and Rainbow Dash's wedding, Princess Celestia left Twilight a message saying that she should prepare herself if something happens. The next morning, Twilight awakens to find that all of Ponyville has succumb to a blinding fog. She must now travel a monster-filled town in search for her teacher and friends and try to return Ponyville back to the way it was.

The royal court of Canterlot welcomes its newest member with open forelegs: the human philosopher Voltaire, from Earth.

On Earth, Voltaire is known as the greatest enemy of tyranny in the history of literature, and a legend in his own mind.

On Equestria, the court betting pool is giving him a week before the Princess banishes him to the Moon.

Note: This story doesn't have sequels per se, but there are a couple of short follow-ups set in the present day ("Parade Coverage" and "Secret Histories"), and a prequel of sorts in "At the Inn of the Prancing Pony".

TV Tropes page.

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

This story is a sequel to Too Shy for a Rainbow

If you liked this fic, check out the awesome Audio Dub version of it by The Lost Narrator!:
https://www.youtube.com/playlist?list=PLnqCBZacYIwK0xcHv85Lke-xFf5V9p7R4

It's been a month since Fluttershy and Rainbow Dash started dating. Everything was going fine until Fluttershy started experiencing horrific nightmares that started keeping her up at night. Looking for answers, Rainbow Dash, Fluttershy and Pinkie Pie seek out Twilight. But when the three mares find themselves within the world of Silent Ponyville, will things turn out for the better? Or will things end in tragedy?

Sequel: http://www.fimfiction.net/story/14866/Silent-Ponyville%3A-Reunion

One rain-filled day, five hundred years after becoming a Princess, a lonely and depressed Twilight takes an unguarded moment, away from her responsibilities and reflects on all the friends that have left her behind.

Cover art by SlyGuyMcFly.

This story is a sequel to Post Nuptials

In the aftermath of the wedding, Spike is bitter and avoiding everyone. Twilight's determined to find out what's bothering her charge, but she walks a very fine line when dealing with an emotionally distraught child.

Meanwhile, Rainbow Dash suspects something's wrong with Scootaloo, so she starts spending more time with her in hopes of picking the secret from her brain. As she begins to truly mentor the young filly for the first time ever, she begins to see the advantages to having a little sister.

And while all this is going on, Pinkie is struggling with some old family issues that have been brought to the surface, meaning she might have to confront her past at last.

Art by Conicer

This story is a sequel to The Dresden Fillies: Strange Friends

Almost a year has gone by for Harry Dresden since he left Equestria. He'd have written, but between saving his newly discovered brother and destroying a scourge of vampires he's been a little busy. Then out of the blue he receives a strange letter from Twilight asking him to return. With no cases at the moment he eagerly accepts, but his friends aren't the only ponies expecting him. There's been a lot of rumors since his last visit and some ponies aren't too keen on seeing him come back.

A sequel to The Dresden Fillies: Strange Friends.

This story is a sequel to Into The Depths

The horrors of the catacombs have turned to distant memories for Celestia, Twilight, and Luna. Discord’s change of heart and Twilight’s coronation have helped to ease and erase the mental scars from that harrowing night. The three princesses can even smile and laugh as Nightmare Night moves into full swing.

Yet, it should never be forgotten that those who have been touched by Tirek are forever within his grasp.

The star system Omega Centauri was just another oddity on a map to scientists in the not too distant future. However when they found the star was orbiting an earth-sized, earth-like planet instead of a black hole as its motion had suggested, a mission was scrambled to investigate this most unusual of celestial behaviors.

Hamstrung by politics, and nearly crippled before it began, the 'Lone Ranger' mission was reduced to just one crew member and left to his own devices.

These are the logs of Arrow 18 and its lone commander. This information is classified TOP SECRET by the Global Space Agency.

Do NOT tell the princess.