List is now mirrored to the thread List of Transpony Stories On And Off Fimfiction I just started on the Transgender Bronies group.

Last updated August 16, 2014.

There are some transpony stories out there (both on FimFiction and elsewhere) but they can sometimes be hard to find, so this is a compilation of all the ones I have found through extensive searching. If anyone knows of one not on the list, I would be happy to add (assuming it isn't too problematic with no redeeming qualities) it to the list.

Be warned, many contain some cissexism to varying degrees in the stories on the parts of the characters within them (hard to tell whether it is on the author's part or not in some).

First, sets of stories that are in the same universe.

A set of five stories starts with an OC transmare has to run from her home and is found, injured, by Applejack in Ponyville. Warning, contains violence targeted at transponies.
Dysphoria, Arc 1: Introductions
Dysphoria, Arc 2: Ponyville
Dysphoria, Arc 3: Canterlot
Dysphoria, Arc 4: Summer Breeze
Dysphoria, Arc 5: Equestria
Also pay attention to the Dysphoria Group as future stories in the same universe will be added there.
Then there is the side story (of Baltimare, Arc 5) by wispin. Sunspot is a questioning young colt (or filly, or perhaps something else entirely) seeking answers from Evening Rose and the Equestrian Equality Envoy. Warning: contains transphobic violence including from a parent.
Dysphoria Chronicles: Sunspot's Flight

Glitter Shell (transfilly Snails)
There is the tumblr where she started from. Note, the author uses the word "trap" in a problematic way at one point as part of the mod comments.
Ask-GlitterShell.
Then there is the story on here where she has faced considerable rejection and goes in search of Trixie hoping to find somepony who will accept her.
All That Glitters

Scotchtavia
Transmare Octavia story where she accidentally tells her girlfriend Vinyl Scratch about her history when she is drunk.
Scotchtavia
The Morning After

Now, for single stories on FimFiction.

Transmare Rainbow Dash coming out/being found out to the mane 6 and her parents and the beginning of her foalhood trials (the author is working on finishing that part).
Dash's Secret

Princess Celestia (in the present) is a transmare dealing with her past and how she has been in stealth for over 1000 years. Story currently in progress.
The Sun may Rise, but the Daughter reigns

Genderqueer Octave Symphony (we know them as Octavia in the show) is dealing with life as a non-binary earth pony in Canterlot. Also features trans colt Record Scrape (we know him as Vinyl Scratch in the show). Story contains some discussion of sexual characteristics and sexual themes. Story currently in progress. It recently changed to NSFW, so I am breaking the link due to the new rules on FimFiction. So, I am giving a link with a mistake in it and telling you how to fix it. In the part that looks like a link, change the ++ to a //.
Mezzo
http:++ www.fimfiction.net /story/138743/mezzo

Scootaloo is a transcolt who is trying to transition and is facing many difficulties from other ponies. Story is still in progress.
In the Wrong Body: The Tale of a Transcolt

Hearth Fire (OC) is a transmare who is still stuck living mostly as a stallion. She has talents she can't share yet, but Rarity notices. Also contains a slight reference to Glitter Shell. Story is in progress.
The Mirror and the Mare

High Style (background fashion pony who works for Photo Finish) is a transmare and is dealing with loneliness in her stealth life.
The Scandalous Secret of High Style

Fluttershy is a transtallion and comes out to the mane 6. Story is still in progress. Fluttershy the Transcolt

Transmare Big Macintosh conteplates her situation and decision to live as a stallion out of duty.
Things Birth Denies

Spike coming out as not a dragon and not male.
Strange Reflections

Babs Seed is a trans colt, but really wants to be seen as a colt but can't tell anypony, and also might have an interest in fillies. Short story with Diamond Tiara and Silver Spoon.
Kissing Practice

The spa ponies are both trans mares struggling with their genders while growing up, not knowing of each other's secrets at first.
Destinies Entwined

Trans stallion Silver Spoon story where he writes an article for a magazine about how he went from being the filly henchman of Diamond Tiara to not being a bully anymore and transitioning.
My story from blind follower, to leader of my own gender. A silver Spoon story

A questioning Scootaloo story on the beginning of the path of questioning gender.
Scootaloo's inquisitive question to herself

A trans stallion AJ story where she reflects on her situation and life and her worries about coming out.
The true me I see in the mirror

Trans mare Rarity comes out to Spike as they are beginning to date. Also has another chapter where she comes out to Fluttershy when she is stranded during a storm.
A Truth So Elusive

Applejack is a trans stallion getting his transition going. The story is a therapy session with his gender therapist, Twilight Sparkle.
Fix You

Rainbow Dash comes to realize he is a guy and decides to tell his other friends after talking about it with Pinkie Pie and Rarity.
The Real Me

OC transmare still living as a stallion coming to terms with it and coming out to her friends, family, and coworkers and the trials that leads to. Be warned, this story involves violence towards transponies and weapons.
Her Life, In a Pan

A background stallion's foal (OC) is a transfilly who comes out to him and they begin working things out for his daughter (not finished yet).
Stallions Don't Cry

Transmare Fluttershy comes out as a transmare to the mane 6.
Fluttershy's Secret

Rarity's foal (OC obviously) comes out to her as a transfilly and Rarity helps her present as female for the first time to go to the gala, which doesn't go well. The story is incomplete and given the last update time probably won't be finished. Be warned, this story contains sexual assault and attempted rape.
Rarity's Jewel

A bit of a problematic story (it has "Trapping" in its title for one and has a few other cissexist and transmisogynistic elements) that has some redeeming qualities on those same fronts about a transmare background pony, Hairspray, and a background stallion, Quarterback, falling in love with each other. I thought about not putting this up on this list for the longest time, but decided I needed to keep my list comprehensive and the story isn't completely problematic (as I said, it has a few redeeming qualities).
Trapping the Quarterback

Now for the ones that aren't on FimFiction.

First, a collection of 4 transpony stories, 2 plain old sexswaps, and one species swap. They were for a 30 Minute Ponies. Specifically it is Prompt 332: “These Things Aren’t Binary". And now for the stories one by one. Two trans stallion Fluttershy stories.
"Courage" by Donnys Boy
"Beauty" by Atosen
Genderqueer Big Mac.
"Inferential Distance" by tlantzn
And a not really specified Pinkie Pie (has a few mild sexual references).
"Piorities" by rwlart

First, a story that is not technically about being transgender, and is instead about Spike getting into makeup. There is some overlap in the experience though, so that is why I am adding it here. And of course there is the possibility that Spike might be trans and not put it together yet, but that is not a foregone conclusion.
Trust Falls and Trust Fails

The brief transmare fic I had thought was lost was recently found (thank you ultimate for finding it.).
Bleed Like Me

Transtallion Rainbow Dash comic on Deviant Art (not yet finished).
Rainbow Dash TG

Transmare Rarity comic on Devient Art (not yet finished). It is in an R63'ed world.
Transition

There is a genderqueer or bigender trans Pinkie Pie/Bubble Berry story on tumblr. It is NSFW with serious clop just so you know. I was wary because sexualized anything with regards to trans people is usually pretty bad and the same would extend to ponies but it was actually quite respectful. Odd way for Pinkie Pie/Bubble Berry to figure it out though. Also, due to the new rules on FimFiction, I have to change the link so it is no longer intact. So, I am giving a link with a mistake in it and telling you how to fix it. In the part that looks like a link, change the ++ to a //.
Bubble Bath
http:++sextyminuteponies.tumblr.com/post/36896423922/prompt-41-bubble-bath-by-daydream

There is a bigender Hoity Toity story that is on google docs.
An Outfit for Every Occassion

Transstallion Rainbow Dash comic on Deviant Art. Particularly noteworthy for Dash's facial expressions.
Trans Ponies