These stories here are awesome. If you don't like human or crossover fictions, then try these.

It's a Dangerous Business, Going Out Your Door

It's definitely one of the best normal/adventure/epic fanfic (now on FimFiction!).

Sunny Skies All Day Long

It's a very good short and normal fiction. Must read!

Flitter

A wonderful executed story; it explains a lot of things about changelings, almost like a canon episode.

Mort Takes a Holiday

Even the Mane6 can be friend with Death itself... but they still don't know it.

A Novel Tale

I just love the way this story explains changelings' nature while narrating a good story.

Cloud Stories

This is a wonderful performed short story; it could almost be an episode.

Lost Cities

Epic (and short) scene description and worldbuilding story.

It takes a Village

I don't usually like Spike's fictions, but when I do they're awesome and excellently written.

The Good, the Bad, and the Ponies

I'm breaking my personal "no-pony must die" rule with this one, but you have to expect it if you decide to read a good perfect [Western] fiction. And just ignore the [Dark] tag: it's misleading.

Integration

Even background ponies like Caramel can be magnificent characters. This story explores the conflicts and contraddictions between ponies and changelings using an awesome storytelling and a good amount of feels.

Tales of the Tutelary Spirits

Lessons Learned from Loyalty
Truth Earned from Honesty
Wealth Granted from Generosity
A brilliant future universe in which our Mane6 represent the embodiment of their respective element. This stories are awesome,'nuff said because I really like how the author managed to balance real life stuff, worldbuilding and hope for the future.

If there is one fiction that piqued your interest in this list, then don't be afraid to read it.

Drop of Moonshine

Go home Celestia! You're drunk!.

Number 12

If you're a Doctor Who fan and you're looking for a good crossover, then look no further.

White Box

Just watch and listen to this video and see if you want to know how it ends.

Hard Reset

If you're looking for a dark fiction with a relatively happy ending then try this one: you'll be horrified from what Twilight has experienced, but later on you will rejoice when it will all be over.

Huggled

[Random]+[Comedy]+coherent story = a very funny short fic about zombiehug ponies.

Night Guards

This is a nice story if you want to read something about Luna and her past (and especially her two bat-guards).

In Her Majesty's Royal Service

This story about royal guards has a very curious and enjoyable sense of [comedy] while mantaining a good [slice of life] feeling. It has also a very lovely sequel.

The Night Guard - Night Mares

The royal guard is recalcitrant to accept mares in their ranks; let's see if Luna and four elite mares can change that. Excellent characters' development here.

Fly and Fall

Written by the same author, these two are perfect second person short fictions.

Mash Effect

A Mass Effect crossover done right: it's clever and original. The author is a renowned one, so ignore the butthurt's downvotes: they're just that.

A Legion Of One

Legion (from Mass Effect 2) meets filly Twilight in a very plausible crossover. There will be lots of good feels.

Book of Days

Twilight Sparkle translates Clover the Clever's diary concerning the early life of Princess Celestia and Luna.

The Sun Burns Brightly and The Moon Glows Gently

Two intertwined short stories describing the two sisters' personalities when brought to their respective opposites. They're both cute and sort of serious/comical.

Funatics

Another little story recounting the wonderful relationship between Celestia and Luna.

Fur and Feathers

As always, one of Twilight's spells goes awry; the pets' characterization is very well executed.

The Sweetie Chronicles: Fragments

This story here proves that even a little filly can be a great character; the amount of [crossover] with other fictions is also very high.

Eclipse

Celestia and Luna depart for an epic journey to retrieve the Moon in Tartarus. Very good characterizations here.

Off The Edge Of The Map

A well written adventure story (and, despite the Romance tag, there is no shipping). It has also two good sequels.

Thrown Abroad

What could happen if a changeling finds himself alone in the little town of Ponyville?

Mendacity

Bon Bon is a different changeling and she will do anything to protect Lyra from Chrysalis; very high amounts of mithology here.

Bonafide

A short but awesome [Romance] fiction involving Lyra, Bon Bon and a changeling Bon Bon.

Queen of Queens

This isn't your usual changeling fiction; this is a story about a queen with only 20 years to live and her eons old subjects.

The Three Sisters

What if Rarity was always a changeling queen (a particular one) AND the element of generosity.

Of The Hive

I don't usually like changel-ifications, but this different Twilight in this alternate universe can produce a unique story about changelings and their particular society.

The Enemy of My Enemy

Another really good changeling one-shot fiction (if you don't mind the snippet of [Romance] at the end).

Breaking News and Weather

A Rainbow Dash story told using the newspapers.

The Archer and the Smith

A very well executed one-shot story; however, Lyra will need more than one shot to take down The Sorceress' Dragon.

Petriculture

A nice headcanon concept involving Pinkie Pie and Surprise.

An imaginative Performance

A good fluent [slice of life] story involving Applebloom and a musical play.

Special Relativity

Pinkie, AJ, Rainbow and Lyra understand what it means to be a family.

Roll for Initiative

What if the Mane 6 would like to play some D&D?

Cards Against Equiniti

If you have played Cards Against Humanity then you know what to expect. Just a note: Fluttershy wins.

Sky Pirates of Equestria: Phoenix Flight

Mane six as (good) sky pirates in this universe themed one-shot fiction.

School of Hard Knocks

A very well executed detective story with a filly stallion as main protagonist; written by the wonderful Hoppy McGee.

The Terribly Taxing Tribulations of Twilight Sparkle

[Comedy][Random]; ponies don't like to pay taxes, that's for sure.

Words Failed Her

An original short and pleasant adventure involving Twilight Sparkle.

Heads in the Cloud

A nice adventure fiction that attempts to explain how ponies get such predictive names.

Journeyman Speech Level Achieved!

If you are a fan of Krieg from Borderlands 2, then you have to read this short fic.

Fridge Horror

Lots and lots of Pratchett's comedy style here; I never laughed so much only because Derpy failed to make a sandwich. XD

The Striped Pony

A rare (because it's good) Zecora fiction, one that shines in its simplicity.

B.B.B.F.F.B.R.

Let's find out who is the best big brother best friend forever. Recommended for its comicity.

A FLEet|ng LIght |n thE DArknEsS

A well written horror story involving Ponyville. The sequel is also worth a read.

Appletheosis

The Snake and the Apple; Applejack and her friends; I actually can't find an exact definition for this fic, but it's worth reading.

A Mighty Demon Slayer Grooms Some Ponies

It's dark ("real life" type of dark) and it's sad, but this interpretation of G1 works too damn well.

The Best Night Ever

This one is an old classic: Prince Blueblood in an excellent reenactment of Grounghog Day.

Twilight Sparkle vs. The Haunted Mailbox

It's just a normal day in Ponyville: the sun shines, Pinkie is worried about RD letters from the Wonderbolts academy and Twilight fights off an evil mailbox.

Minuette's Lesson

A short Sweetie Bot story questioning life.

Transistance

A good science-fiction set a thousand years in the future, starring Luna. The princesses may be a little OOC from your point of view, but a lot of time and technologies can change somepony.

A Draconequus' Guide to Immortality

An original story about Twilight's immortality? without the usual clichés about this theme.

Moonlight

A very awesome adventure fiction with Scootaloo as main character (also: Luna!).

Don't Knock It Till You Try It

A very good [Slice of Life] fiction with Rarity and Rainbow Dash.

A Moment in the Sunlight

A cute short [Slice of Life] story with Celestia.

Never So Far Away

Nice little [Slice of Life] interaction between Twilight and Celestia: sometimes we just have to remind ourselves what really matters.

I'm a Cat!

This is just a cute little story: it is so sweet that you will need insulin shots... a lot of them. Now there is also a sweeter sequel with Fluttershy.

Rainbownomicon

Just a bit of good dark comedy.

Big Horseshoes

[Slice of Life]; Rumble and Thunderlane need more brony love.

On a Cross and Arrow

The original Rule 63 fiction that spawned all the others.

Applejack's Bar

A nice little normal story about AJ.

On The Importance Of Spelling

A cute little moment with CadenceCadance and Shining ArmourArmor.

Ghosts

An interesting little story about bat ponies and their origins.

The Firework Lotus

Change can hurt, but it's how we perceive it that truly defines change. A short story about Spike and Twilight.

Ah Ain't Got no Ack-cent!

The fact that AJ has an accent should really be brought up in an official episode.

A New Perspective

A little story about strenghts.

Scootaling

A short story to define ponies' reactions if Scootaloo was a changeling.

Scootaloo's Father's Day

A little story about Scootaloo's awesome parents (and also the rest of the Mane6).

Random Acts of Generosity

[Sad][Slice of Life]; Rarity's generosity at its finest.

The Elements of Maternity

A cute one-shot fiction where the Mane Six got pregnant and they have to deal with the consequences.

A Roll in the Hay

Exactly what the title says (no clop).

Of Birds and Bees and Awkward Things

Yes, I'm hiding this fiction at the bottom of the list. No, it's not a clopfiction. Yes, Celestia gives teen Twilight "the talk". Overall, things get pretty cute and awkward.