Nowadays, it's my opinion that scrolling through literally thousands of story listings in an effort to rip something worth reading out of the jealous clutches of Sturgeon's Law generally is not worth my time. Some years ago, however, that was not the case. Following is a list of fanfiction stories that I've bothered to save in EPUB format. (Nowadays, I tend to prefer raw HTML over EPUB. There are quite a few stories that I've downloaded in HTML format but have not yet bothered to clean up for final archival. Such stories are not listed here.)
Any notation other than the title is haphazard. An explicit endorsement of one story should not be interpreted as disapproval for other stories. An explicit mentioning of one author should not be interpreted as an admission that I don't know the identities of the authors of other titles.
If the author of one of these stories has been pathetic enough to attempt to scrub it from the Internet (e. g., Tozette), feel free to ask me for a copy of the file.
Avatar
Dynasty of Storms
When the World Stops Spinning
The Game Has Changed
Ripples in the Water
Imagine the Ocean
Imagine the Ocean
Listen to the Earth
Bad Ends
Embers
Future Echoes
Life Bound
Snow (part 1)
Stalking Zuko (an interesting case of how the framing story can excuse bad English)
Stalking Zuko
Not Stalking Zuko
Not Stalking Firelord Zuko
The Boy from Babel
West Virginian Yankees in King Bumi's Court
Ben 10
Little Moments
Little Moments
Breaking Point
Parentheses
Rewind
DC
Inviolate
The Metropolitan Man
Death Note
Genius Is a Curse
Short stories featuring Light/Sayu incest
So Hide Your Eyes
Deviant Behavior
Deeper Than Just Blood
Hatred
Friendship Is Magic
Austraeoh (I think I only read the first two or three of these)
Austraeoh
Eljunbyro
Innavedr
Odrsjot
Urohringr
Yaerfaerda
Ynahluutr
Fallout Equestria
Fallout Equestia
Project Horizons
Pink Eyes
Friendship Is Optimal
Friendship Is Optimal
Heaven Is Terrifying (Caelum Est Conterrens)
Psychopathy Is Configurable
Hard Reset
Hard Reset
Reset Harder
The Reign of Queen Twilight Sparkle
Megapone
Her New Role
Please
Too Big (the only story in the Pleasured collection that I bothered to save)
Of the Hive (I think I only read the first one or two of these)
Of the Hive
For the Hive
Aegis of the Hive
Culling of the Hives
The Piano Man
The Signal
The Signal
Frequencies
Then Tomorrow Came
Background Pony (at one point in history, beat out Time Braid for the position of my favorite story ever)
Beating the Heat
Contraptionology
Eternal
Friendship Is Mind Control
I Am Not the Actor
I Forgot I Was There
Let's Be Evil
Miss Sparkle, Psychopath
Rainbow Dash Discovers Erotic Mind Control
Romance Reports
The Best Night Ever
The Numbers Don't Lie
The Unexpected Love Life of Dusk Shine
Triptych
Xenophilia
Harry Potter
Black Queen
Princess of the Blacks
Black Princess Ascendant
Firebird
The Firebird's Son
The Firebird's Song
The Firebird's Fury
Harry Potter and the Methods of Rationality
Harry Potter and the Methods of Rationality
Ginny Weasley and the Sealed Intelligence
Magisterius University and the Methods of Obstinacy
Almost a Squib
Always and Always
Harry Potter and the Natural Twenty
Harry Potter and the Power of Paranoia
Harry Potter and the Temporal Beacon
Brutal Harry
Business
Chary Potter and the Years of Reluctance
Concentric Wavelengths
DID You Hear the Rabbit Cry?
Eden
For the Price of a Soul
Getting the Hang of Thursdays
Harry the Hufflepuff (books 1–3)
Hit the Ground Running (Tozette)
Holly Evans and the Spiral Path
How Fleur Delacour Seduced Me
Knowledge Is Useful, but Power Is Power
Life Lessons
Nightmares of Future Past
Oh God Not Again
Partially Kissed Hero (ignore the haters)
Prince of the Dark Kingdom
Remus Lupin, PI
Seventh Horcrux
Sisyphus
The Birth of Evil
The Hogwarts Strike Team
The Scarlet Pimpernel (starring Percy Weasley!)
The Two-Body Problem
Tied for Last
Unspeakable Things
Veritas Oracle
War Paint
When in Doubt, Obliviate
Wizard of the Kaleidoscope
Lord of the Rings
At the End of All Things
The Last Ringbearer (meh)
Naruto
In the Blood (second-favorite Naruto story)
A Teacher's Glory
Addiction
Chunin Exam Day (ignore the haters)
Dirt and Ashes
Fixed Idea (Idée Fixe)
Freedom in the Eyes of Another
Introverted
Invisible Fox
It's Just That Any One of Us Is Half without Another One Is You
Maybe Next Time
Naruto GOTY Edition
Naruto's Compensation
People Lie (probably third-favorite Naruto story)
Plucking Strings
Ramen Days
Riding the Echo Down
Rosemary for Remembrance (nostalgia for one of the first fanfiction stories I ever read)
Scorpion's Disciple
Study of the Heart (nostalgia for one of the first fanfiction stories I ever read)
Team 8
Team Anko
Team Seven's Ascension: Blood Wings
The Boy in the Team
The Cost of Living
The Empty Cage
The Eyes Have It
The Ghost and the Darkness
The Waves Arisen
Time Braid (nostalgia for one of the first fanfiction stories I read; my favorite story ever)
Trapped in the Amber of This Moment
Vapors
Visionary
Vulpine (cute homage to Time Braid)
Star Wars
An Origami Fish
A Destiny Altered
Caught between Destiny and Fate
A Fate Unseen: Swarm War
Fate's Betrayal
Instruments of Destruction
The Force Awakens (Max Landis)
Only Right
The Last Jedi (Darth Marrs)
The Truth of the Sith
Teen Titans
Doppelganger Non Grata
Robin Has a Heart Attack
Worm
Memorials
Cenotaph
Wake
Setanta
Crime and Commitment
Manager
Silencio
Weaver Nine
A Bluer Shade of White
Branches on the Tree of Time
Cold and Dark
Connecting the Dots
Legit
Little Green Men
Luminosity
Luminosity (meh)
Radiance (cool)
Flashes
The Other Side of Tomorrow
The Two-Year Emperor (meh)