Quizzical Greystone has just come to Ponyville as an assistant in Friendship Research. Such a socially inept filly might not be the best pony for the job. But this just might be the job she needs. If you can't make friends in Ponyville can you make friends anywhere?

Dear Princess Celestia,

I'm sorry I haven't written in a while. Things seem to be falling through the cracks lately. Spike thinks I should go see the doctor, but...

Bon Bon's voice is funny, and that's about all that anypony who meets her notices, as her marefriend Lyra soon steals the spotlight with her explosive personality, strange obsessions, and curious beliefs. And why not? Bon Bon is, after all, a perfectly ordinary, boring pony in every way but two: her voice, and the carefully kept secret that she isn't really a pony.

(Edit:) Now with an annotated version, courtesy of the incomparable Shoggoth Lord!

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

To Twilight Sparkle and Princess Celestia, it is a simple surprise visit to Canterlot. To the ponies of the Equestrian Civil Service, it is twenty-four hours of chaos, politics, weaponized dessert, politics, underhooved manipulation of media, politics, and things batrachian and tentacular. Who said bureaucracy isn't exciting?

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

Twilight reads about a way to view a pony's soul, to see everything about them laid bare. When she tries it on her friends, will she be able to look at them the same way again? Or will the secrets hidden in their hearts drive her away?

(Yes, I borrowed the idea of a "soulgaze" from The Dresden Files, because it's something that really fascinates me. It's not a crossover, just an idea.)

Now has a sequel!

This story is a sequel to Windfall

A brilliant mind discovers a problem in search of a solution, which leads to inspiration, which leads to invention, which leads to a technological/magical advance that will in time forever change Equestria.

Sequel to Windfall, set three years after the events in that story.

Rainbow Dash attends her hometown's Millennial Summer Sun Celebration, where she meets a peculiar pink pony. When a strange portal appears during the testing of Twilight Sparkle's latest invention, and pulls their new companion inside, the two friends give chase and embark on the most important adventure in all of history.

Equestria Daily | TVTropes

It started out as an ordinary day for Fluttershy – waking up in her house in Cloudsdale and going to work managing the weather for Ponyville alongside her best friend Cloud Kicker. However, she finds herself troubled by feelings she can't explain, feelings that something serious is wrong. When she starts having visions of a strange life with strange ponies, she's determined to find them and find out what's going on. But how can such a timid pony convince others of what she isn't sure of herself?