*Not counting flashbacks, only going by the primary narrative, and ignoring all in-story journals or 'books within a book.'

Before Friendship is Magic:

Distant Past (Before Equestria):

Antumbra
Celestial Coloring
Tranquility
Doomsday Begins Here
Nopony's Daughter
A Blade of Moon and Stars
Promises Frozen in Time
Just Weep
The First Monster
Of Fever Dreams and Falling Stars
Past Skies
The Dark Side of the Sun
Tasting Power
Ashes
How to be Brave
Follow Her Lead
Tear The Sky Asunder
The Storm Dancer
Pri(n)celess
Through the Snow
Bodysnatchers

Distant Past (Before Discord, or During First Equestria):

Defining Features
Behind Red Eyes
Spare Him His Life
Click
The Symphony of Dawn
The Encore of Clover the Clever

Distant Past (Including Before Modern Equestria, or the Start of Second Equestria/Post-Discord):

Last Laugh
Twitch
Breathe
Forever Mare
Nopony's Sister
All the World

Distant Past (Princess Celestia's Solo Reign):

Right/Wrong
Autophobia
Alethophobia
Pale Nights
Deep Blue
Frozen One
Don't You Know the Sun is Coldest When You Touch Her?
Mercy, Celestia
Hagseed and Harlotry
Ichor (Mature Version: Stay Golden)

Not-so-distant Past (A few years before the show/Late Solar Millenium):

On Deaf Ears
So Maybe
Piecemeal Pupil
Atychiphobia
Distance Beyond Any Measure
Storge
Mares, Metaphors, and Maybes
For the Filly I've Never Met
Her Own Sky
Your Porcelain Face
Tuning It Out
Prodigal Sun
Truthfully
Sweet Sleepy Sunshine
Crumb-y Day
Midday Munchies
Merry Munchies
Don't Make a Shadow of Yourself
No Spells Needed
Breathtaking Banality

During The Same Time Period As Friendship is Magic:

Around Season One:

To Their Destruction
This Present Darkness
Barr|iers
Horrible Words
Stardust Bridge
Ivory Tower
Big Little Spoon
Atelophobia
Misery is Company
Philia
Mother Hen Syndrome

Around Season Two:

Shoot For the Moon
Love❤Less
Proverbial Roses
Class Portrait
In Your Kindest Voice
Cadance Comfort
Bathophobia

Around Season Three:

Euphoria, Robbed
Ultraviolence
Nothing Is Real

Around Season Four:

Bat Ponies Aren't Real
The L Word
Heliocentrism
Victory for the Dark Horse
Crystalline:Her Destiny
Noise Pollution
Tomb of Magic
Ballad of the Forgotten Apple
Only Every Time

Around or After Season Five:

Millenium Tokens
Dead Dove (Do Not Eat!)
Some Kind of Nature (Mature Version: Bastard Juice)
The Company We Keep
Divine Move
Stella Aura
Just A Game
Perfectly Arranged
Wishing Werelights
Favorable Alignment

After Friendship is Magic:

With Her Dead Eyed Stare (Mature Version: Halfway Mare)
Too Early
Scrambled Serenity
It's Called Paradise
The Care and Keeping of Hidden Castles
Dressed to Impress
Think Pink (Probably)
Endevors of the Eccentric and Enigmatic
No Surprises, Please
Morning Masterpiece
Enemy of Mine
Érōs
Crystalline Dreams
Remember When