Here's the current list of stories, sorted by category and then alphabetically (except for the Megaverse trilogy). Status is current to 02/07/2019.

The Core - Adventures of the Trained 6 (7 complete, 1 forthcoming):

* Batmare Beyond - Rarity is raised by Bruce Wayne (the retired Batman) of the DC Animated Universe. (Status: Complete.)
* Dante's Little Apple Surprise - Applejack is raised by Dante of the Devil May Cry video game series. (Status: Complete.)
* Fortresshy: The Nine Fathers - Fluttershy is raised by the protagonists of Team Fortress 2 video game. (Status: Complete.)
** Fortresshy 1.5: For(t) Pony - direct sequel to the above; details Fluttershy's time back in Equestria. (Status: Complete.)
* The Technological Technicolor Technomare - Rainbow Dash is raised by Tony Stark/Iron Man of the Marvel Universe. (Status: Complete.)
* The Sparkle in his Eye - Twilight Sparkle is raised by Ratchet of the Ratchet & Clank video game series. (Status: Complete.)
* You Can't Spell Slaughter Without Laughter - Pinkie Pie is raised by Kratos of the God of War video game series. (Status: Complete.)

Forthcoming:

* Apple Far From the Tree - sidestory detailing Applejack's school years attending Death Weapon Meister Academy, Youkai Academy and Kuoh Academy.

Not-So-Bad-Guys - Major villains, both current and former (3 complete; 1 ongoing; 1 forthcoming):

* Order and Chaos - Discord is raised by Sheogorath/Jyggalag of the The Elder Scrolls video game series. (Status: Complete.)
* The Merc With the Moth - Queen Chrysalis is raised by Deadpool of the Marvel Universe. (Status: Complete.)
* There's Nopony I'd Rather Be Than Me - Nightmare Moon is raised by the title character of Wreck-It Ralph (animated film). (Status: Complete.)
* Three Kittens, Two Unicorns, and a Banana - Tempest Shadow/Fizzlepop Berrytwist is raised by Gru, his adopted daughters and the Minions of the Despicable Me animated film series. (Status: Ongoing.)

Forthcoming:

* Shadows and Light (or possibly Between Darkness and Light) - King Sombra is raised by Cecil and Rosa of Final Fantasy IV (video game).

Sidekicks - Everyone else (6 complete; 5 ongoing; 5 forthcoming):

* Another Hatchling - Spike is raised by Samus Aran of the Metroid video game series. (Status: Complete.)
* Dragon Ball Zeeeeyup! - Big Macintosh is raised alongside Gohan of the Dragon Ball Z Abridged web original series.(Status: Ongoing.)
* Dressed to Steal - Coco Pommel is raised by Sly Cooper of the Sly Cooper video game series. (Status: Complete.)
* Heart of the Dragon General - Princess Cadance is raised by General Iroh of the Avatar: The Last Airbender animated series. (Status: Complete.)
* Mother X: Father - Moondancer is raised by Gigue/Giygas of the MOTHER video game series. (Status: Ongoing.)
* My Little Killing Machine - Gilda the Griffon is raised by GLaDOS of the Portal video game series. (Status: Complete.)
* My Own Wings - Sunset Shimmer is raised by Team Star Fox of the Star Fox video game series. (Status: Ongoing.)
* On the Corner of Straight and Narrow - Trixie Lulamoon is raised by the title characters of the Sam & Max video game series (with Max as father and Sam as uncle). (Status: Complete.)
* Sons of Damas - Shining Armor is raised as the brother of Jak of the Jak and Daxter video game series. (Status: Complete.)
* The Rock in the Gulch - Maud Pie is raised by Leonard L. Church of the Red Vs. Blue machinima series. (Status: Ongoing.)
* Three More Things! - The Cutie Mark Crusaders (Apple Bloom, Sweetie Belle and Scootaloo) are raised by Uncle Chan of the Jackie Chan Adventures animated series. (Status: Ongoing.)

Forthcoming:

* Celestia's Log - Princess Celestia is raised by Captain Jean-Luc Picard of Star Trek: The Next Generation.
* DRGN - Princess/Dragon Lord Ember is raised by Team RWBY (primarily Weiss and Blake) of the RWBY web original series.
* On Wings of Fire - Spitfire is raised by Palutena and Pit of the Kid Icarus video game series.
* Starlight Falls - Starlight Glimmer is raised by Stan Pines of the Gravity Falls cartoon series. (Note: May or may not be part of canon, depending on reader response.)
* The Little Angel - Derpy Hooves is raised by Kei and Yuri of the Dirty Pair Flash anime OVA series.

Megaverse - a trilogy based in the world of the Mega Man video games (3 complete):

* Wily's Wittle Wub - Vinyl Scratch is raised by Dr. Albert Wily of the Mega Man (Classic) video game series. (Status: Complete.)
* Melody of the Future - Octavia Melody is raised by the title character of the Mega Man X video game series. (Status: Complete.)
* Denouement Duet - epilogue story to Wily's Wittle Wub and Melody of the Future, depicting Vinyl and Octavia's respective returns to Equestria. (Status: Complete.)

Phase 1 Finale:

* My Little PWNY - mega-crossover in which Discord's timeline and the 22 he split off from it are merged back into one for the climactic battle.

Phase 2 (fics set in divergent timelines, they ignore and will be ignored by My Little PWNY):

* Fortresshy 2 - set after the events of Fortresshy 1.5.
* Power Pony Harmony Rangers - set after the events of The Sparkle in his Eye and focused on Sunset Shimmer and other characters from the human side of the Crystal Mirror.
* PWNYverse: The Cutting Room Floor - an anthology including all the ideas and snippets Tatsurou had for stories that, for whatever reason, he never used.

Until next time...
Anon e Mouse Jr.

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* My Little PWNY - mega-crossover in which all of the Adopted Displaced* are brought to a single universe to team up against an unidentified enemy. Set after everything but Fortresshy 2.

*And their parents/additional adopted family, because that's half the fun of these stories

* My Little Killing Machine - Gilda the Griffon is raised by GLaDOS of the Portal video game series.

that's gonna be good!!!

* (not yet named) - Big Macintosh is raised alongside Gohan of the Dragon Ball Z Abridged web original series.

That sounds... intriguing

* My Little PWNY - mega-crossover in which all of the Adopted Displaced are brought to a single universe to team up against an unidentified enemy. Set after everything but Fortresshy 2.

I've been expecting this to happen sooner or later. Glad to see my gut was right about that.

Just a reminder, all of these (including upcoming ones) are also listed on the series' main TV Tropes page - which can be found here.

Until next time...
Anon e Mouse Jr.

I cannot wait for Mother X: Father. I love the Mother series.

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You forget Dressed to Steal the Coco Pommel story.

5634898 It's number 2 in the "Sidekicks" section. (They're listed alphabetically - the only exception is "Melody of the Future", which is with "Wily's Wittle Wub" due to their sharing a direct continuity.)

Until next time...
Anon e Mouse Jr.

5634691 here's hoping Mac learns to dodge better than gohan

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"AJ, big bruther! Diamond Tiara said ah'm adopted!"
"Ah, crap-baskets..."
"Big MacIntosh! Where'd ya pick up that kind'a language?!"
"Uh...Piccolo 'n all'o them?"
"And just how exactly does a flute play into all this?!?"
"Well..."
"Wait, wait, don't tell me; this's involvin' that time y'went 'n disappeared, right?"
"...Eeeyup."
"'N then y'came back with Gohan here?"
"'N all the rest, too."
"...Whut's a "crap-basket"?"

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DODGE!!!!

5635229 Just wait til they reach Namek xD

My Little Killing Machine, starring Gilda and GLaDOS, has officially been posted! (And added here. First post of the thread has been edited as appropriate.)

Until next time...
Anon e Mouse Jr.

First post has been updated to reflect Order and Chaos having been completed today. (Edit: Also updated the titles for Sombra and Mac's respective stories.)

Until next time...
Anon e Mouse Jr.

First post is updated again. Details are accurate up to and including the launch of Mother X: Father.

Until next time...
Anon e Mouse Jr.

First post updated to reflect Melody of the Future being completed and recent fic announcements.

Until next time...
Anon e Mouse Jr.

First post updated to reflect the release of Denouement Duet.

Until next time...
Anon e Mouse Jr.

First post updated to reflect the completion of Denouement Duet and the release of My Own Wings.

Until next time...
Anon e Mouse Jr.

5634691
DODGE!

First post updated to reflect the release of The Rock in the Gulch.

Until next time...
Anon e Mouse Jr.

First post updated to reflect the addition of three more upcoming titles.

Until next time...
Anon e Mouse Jr.

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My Little PWNY- mega-crossover in which Discord's timeline and the 22 he split off from it are merged back into one for the climactic battle.

Ah knew it!!!

I am very excited for On Wings of Fire and Starlight Falls because those series are some of my favorites ever :d