The 100+ stories listed below are fics that I have read and liked well enough to recommend to others. If you want a slightly more concise list, see Stuff I would recommend...

Some day I may organize the story types a bit better into Dark, Adventure, Comedy, etc. or maybe Completed and In-Progress, but that day is not today. Most of the shipping is in it's own group towards the bottom, but there are a few towards the top that I liked enough to list them under epic instead of shipping. Crossovers are in their own section down there as well.

-- Massive list of Favorite Galleries replaced with a custom box. Not as visually nice as before, but at least I can add more stories now.
-- Haven't touched the list for like 8 months at least, it's still accurate but there are lots of stories not mentioned I would otherwise recommend. Need another solution...

Epic Stories
The Immortal Game - AestheticB
The Flight of the Alicorn - Ponydora Prancypants
Through The Eyes Of Another Pony - CardsLafter
Eternal - device heretic
Contraptionology! - Skywriter

A Cup of Joe - The Descendant
Tangled Up in Blues - The Descendant
A Sweet Taste of Cake - The Descendant
The Best Night Ever - Capn_Chryssalid
This Platinum Crown - Capn_Chryssalid

Windfall - Warren Hutch
Earth & Sky - Warren Hutch
The Turning of the Screwball - The Strange Case of Button Stitch - Warren Hutch
Screwball Mio Amoré - Warren Hutch
Screwball Over - Warren Hutch

Upheaval: Breaking Point - Visiden Visidane
Upheaval: Reckoning - Visiden Visidane
A Dream of Dawn - Starsong
Lacuna - Drakmire
My Little Alicorn - InsertAuthorHere

On a Cross and Arrow - Conner Cogwork
Tales of the Winter Magic Academy - Storytayler
Paradise - SlyWit
It Takes a Village - determamfidd
Duties - Denim_Blue

Daylight Burning - Guesswork
The Ambassador's Son - midnightshadow
The Moonstone Cup - Cyanide
Under The Northern Lights - sieurin
Wild Sky Yonder - Mysecsha

The Sweetie Chronicles: Fragments - Wanderer D
Directive: Grow - Dragon Dreaming
A Rose is a Rose - spacebrony
Growing Pains - Peroth E.
My Choices: Twisted Tales Through Time - koolerkid

Keeping It Simple - Ivory Piano
Darkest Before Dawn - Sessalisk
Arrow 18 Mission Logs: Lone Ranger - AdmiralTigerclaw
The Legend Of Star Swirl The Bearded - Blueshift
Tiny Wings - DeadParrot222

The Star In Yellow - Blueshift
The Final Quest of Star Swirl the Bearded - JohnPerry
Trains, Carriages and Airships - JohnPerry
To Be a Better Stallion - Autumn Wind
Wild, Sweet & Cool - Kwakerjak

Order and Chaos - psychicscubadiver
Our First Steps - Mrakoplaz
Twilight's Best Friend - Blueshift
Treasure in the West - DiveBomb
Visionary - Razorbeam

A Different Viewpoint of Equestria - Christopher28
Fluttershy's Bad "Hare" Day - Pegasus Rescue Brigade
Project: Sunflower - Hoopy McGee
Anthropology - JasonTheHuman
Hard Reset - Eakin

Rainbow Dash and the Treasure of Canterlot - (Insert Pen Name)
A Bluebird's Song - Ardensfax
The Strange Destiny of Prince Blueblood - Kavonde
Hostile Takeover - Coconutswallow
Post Nuptials - Darth Link 22

A Slice of Life - Dawnscroll
The Powers of Harmony - CyborgSamurai
Past Sins - Pen Stroke
My Little Mages: The Nightmare's Return - Wragnaroq
The Powers of Harmony -

Shades of Grey -
Whom the Princesses Would Destroy... -
Darkest Hour -
The Sweet Meet and Greet -
Out of Touch -

Half the Day is Night -
The Dread Chitin -
Outside the Reaching Sky -
My Little Pony's Little Ponies - Baby Boo
Flitter - Nyerguds

Background Pony - shortskirtsandexplosions
Never - shortskirtsandexplosions

Epic Stories - Not on FIMFiction
Fallout: Equestria - Through The Eyes of Another Pony (pre-revision) - It's a Dangerous Business, Going Out Your Door - CRISIS: Equestria - Beyond Judgement - Spirits of Harmony

Favorite Short Stories
Princess Celestia Hates Tea - Skywriter
Heretical Fictions - Skywriter
Beloved - Skywriter
Two Ponies - TwilightSnarkle
Old Friends - RBDash47

Sparkle's Law - AestheticB
Pirates For A Day - DawnFade
Sunny Skies All Day Long - PhantomFox
My Faithful Student - PhantomFox
Spitfire's Day Off - Artimae

Finding Your Voice - Kobalstromo
Naked Singularity - Cold in Gardez
For the Love of Science - Cold in Gardez
The Song of Syhlex - The Descendant
Shine - The Descendant

When Duty Calls - ChappyHooves
Maiden Flight - Cold in Gardez
Petriculture - Kwakerjak
Through the Eyes of the Hurricane - Impossible Numbers
The Fires of Friendship - Ponydora Prancypants

My Funny Sister - Pascoite
Shipping Goggles - AbsoluteAnonymous
Pinkie Watches Paint Dry - AbsoluteAnonymous
The Light Goes Out - AbsoluteAnonymous
The Light Never Goes Out - BrianBlessedPony

Drop of Moonshine - Pen Stroke
A Perfectly Ordinary Day in Ponyville - The Equestrian Gentlecolt
For Her - Pyre
And the Temptress Came Unto Her - device heretic
Sword, Hammer, Stallion - RedSquirrel456

The Promises We Keep - Pascoite
Trouble Sleeping - Lurks-no-More
Mothers - KnightMysterio
Lament of a Spoon - Zytharros
Words Failed Her - Nonsanity

The Three Sisters - Wanderer D
Two Peas In A Pod - Blueshift
The Fraternal Brotherhood of Mann - (Insert Pen Name)
Her Weight in Affection - Stonershy
Daring Do and the Pyre of Peril - Warren Hutch

Reading Rainbow - Corejo
Correspondence - Friendly Uncle
A Teacher With No Class - Kavonde
The Good Ship Lifestyle - A Hoof-ful of Dust
Twi Hard 2: Twi Harder - Arcainum

A Differing of Opinions - CardsLafter
Mood Wings - Tchernobog
Pip - Invictus
Applejack's Bar - Alaborn
Quite Ready for Another Adventure - Tamar

A Teatime Visit -
Who We Are -
The Archer and the Smith -
Short Cakes -
The Boneyard -

The Keepers of Discord -
Statistics - xTSGx

Favorite Short Stories - Not on FIMFiction
My Sister Fluttershy

Favorite Shipping Stories
A Camping We Will Go - Trinary
Apples'n'Wrenches - Captain Lackwit
At Home on the Range - Bronius Maximus
Butterflies In Her Stomach - Wragnaroq
Those Blue Wings - Tchernobog

How to Woo Your Lady in Nine Easy Steps - paleowriter
The Ballad of Twilight Sparkle - Gravekeeper
Advice - device heretic
To Be a Better Stallion - Autumn Wind
Triple X - ElMikkino

Fixing Up Miss Smartypants - Arkensaw Pinkerton
Three Magics - Arkensaw Pinkerton
Hands - Andrew Joshua Talon
Love Letters - Tealove
It's Always Sunny in Fillydelphia - Bobcat

Tears in the Snow - Cerulean1313
The Risks of Braving a Storm - Cerulean1313
Unplanned Parenthood - Cerulean1313
Under the Starry Skies - Cerulean1313
Song of Whispers - Cerulean1313

Transcend - Anonymous Pegasus
Robotic Stallion Big Lugnut - HoovesLikeJagger
Sparkling Cider - NightsGlory
Kindness's Reward -
The Traveling Tutor and the Librarian - Georg

Favorite Shipping Stories - Not on FIMFiction
The Lucky One

Favorite Crossover Stories
Magical Pony Lyrical Twilight - PurpleProse
Halo: On the Wings of Angels - Gyvon
World of Ponycraft - Capn_Chryssalid
My Little Avengers - koolerkid
Aitran - CTVulpin

Binky Pie - Miyajima
Guardians of Magic - Shire Folk
Choose Your Own Adventure: Lyra’s Quest - Wanderer D
Foreigner - Salnax
Dragon Tales - Bronius Maximus

A Foul Light Shines -