This is a list that alphabetically organizes gives viewers access to stories with the different types of monster mares. Stories that are NSFW will NOT be included in this list (but maybe in a future list if anyone else is interested).

If you have a list you would like to see or a story you would like added to the list feel free to post a comment below.

Alien-pony:
A Monstrous Meeting of the Fourth Kind

Argapony:
All Eyes on You...
Under the Mistletoe

Basilisk Pony:
A Monster Mare's Exciting Day*

Bee Pony:
Bee Afraid!

Cat Pony:
Klaws and Kat Tails <--From what I could tell, the character is female.

Chimera Pony:
Missed Stop, Monstrous Meeting
Under the Mistletoe

Diamond Dog / Werepony / Timberwolf Ponies:
Night of the Werepony
Sweetie Pup
Timber-Jack
The Werepony
Werelight Shine

Doll/Puppet Ponies:
Miss Smarty Pants gets a life
My Personal Hell - Mischief Patchwork
The Adventure of Fillynocchio

Draconequus/Pony Hybrids:
Magical Mystery Oops
Your Best Shot

Dragon/Pony Hybrids:
All That Glitters
Dream Sickness
Flamelight's Drider Encounter <--Also includes a Spider Mare.
Flames of a Different Type
Growing Up with Scales
Love Sickness
Twilight the Hybrid

Dryad/Plant Pony:
Creeping Happiness
ROOTS
What if Biollante went to Equestria? <--A plant monster from the Godzilla universe turned pony... okay.

Eldritch Pony:
Call of Cthulhu-Shy

Frog Pony:
The Shroomlock of Monster Mares*

Genies:
A Friend Like Trixie
I Dream of Twilight Sparkle
Undisclosed Desires <--Probably want to keep an eye on this one. For the most part it is SFW... for now.
Wish Fulfillment

Ghost-Mares:
Ghost
Ghostly Spells of the Night
Not So Alone After All
Sweet Treat
The Ghosts of Harmony

Ghoul Pony:
Rainbow the undying
Undead Robot Bug Crusaders
Undead Robot Bug Crusaders: Unusual Lives

Golem Pony:
Heart Of Clay*

Gorgony:
Cruel Mercy
Finding Inspiration
Ghastly Weeping Willows <--Also has a ghost mare.
Snake Party
Snakes, Tricks and Treats
The Gorgony in the Everfree
The Librarian's Guide to Gorgonies
The Sculptor

Harpy Pony:
The Shroomlock of Monster Mares*

Kaiju Pony: <--Mares becoming giant monsters!
Daughter of Godzilla
My Little Pony; Kaiju Rumble
The Kaiju Heir

Kelpies:
Beneath the Surface*

Lamia: <--Not to be confused with Gorgon Ponies (Gorgonies).
A Little Lamia
Camp Cobra
Kalianne meets Anon
Kingdom of Monsters
Lamias and ladders
Melody Breeze's Lamia Encounter
Miss Hiss and the Dizzy Minion
My Luna Lamia <--It's My Little Dashie, except with Luna... and she's a lamia.
Serpentine music
Snakepony Salutations
Snakity
The Lamia Queen
The Sweetest Snake
To Love a Hybrid

Lich:
Flutterlich
Rarity and the Phylactery

Moth-pony:
Fallout Equestria: T is for Train
Ordeals in the Hollow Shades

Mushroom Pony:
SHMM: Fairy An-tricks
The Shroomlock of Monster Mares*

Nuckelavee:
Rarity and the Nuckelavee*

Octopony:
Somewhere, Beyond the Sea

Owl-Pony:
The Night Bird*

Salamander Pony:
The Shroomlock of Monster Mares*

Scorpion-Pony:
The Lone Hunter

Seapony:
Daughter of the Sea
Drifting Down the Lazy River
Fish and Lilypad
The Little Mermare
The Seaponies

Shark-Pony:
Beached
Is a Shark Mare's Bark Worse Than Her Bite?

Skeleton-Pony:
Princess Skellinor

Slender-Mare:
What a Horrible Night to Have a Curse

Slime-Pony (or Goo-Pony):
Amorphous: The Tale of Arcades the Immortal
A Goo Day to be Alive
Beware! The Appleblob
Slimed
That Time Pinkie Pie Was A Slime All Along*
The birth of Achlys
The Slimes' Way

Snallygaster:
Schneller Geist: The Demon of Hollow Shades*

Soda Pop Ponies: <--Because apparently this is a thing. Not that I'm complaining.
Mixing Flavors

Spiderpony:
Arachnity
Ask Graceful Thread
The Legend of the Arachnapony

Sphinx:
A Game of Riddles
Airship Mauled
Daring Do and the Sphinx's Treasure
Pharaoh Moans
The Riddle of Origin

Succubus Pony:
Dream Date

Symbiote Pony:
Nightmare

Tatzlpony:
And Thus, I Became a Tatzlprincess
How to Train your Tatzlpony
What is a Tatzlpony?

Tantabus Pony:
Aunthood Issues
How the Tantabus Parses Sleep
Tantabus Communication Protocol
Tantabus, Mk. II

Thing Pony: <--Think the Thing, only it's a pony.
Thingy's Haloween

Vampony:
A Batty Surprised
A bat in pony fur
A Dash Into Blood
Bound By Blood
Corruption
Creature of the Night
Cursed Crusader
Cursed Crusaders: Outset
Meet the Apples
Misunderstood
Path of Kindness and Blood
Twilight: The Last Vampony
Twilit Blood Pact
Vampershy
Vampire Night I

Witches: <--While not technically monsters, depending upon their lore in the story they could be considered "monstrous enough" to fit this section. Can't be a simple unicorn that is using magic.
Ask Roseate Grimsbane, the Witch <--Also has a Succubus and Cyclops Pony.

Yokai:
Why so Serious?*

Zombie Ponies:
Beautiful Corpse
Monsters Can't Cry
Twilight is a Zombie
Twilight's New Nightmare Night Costume
Zombie Shy

*-This represents an entry for the current contest. This allows the judges to know that this story was added to the list as a result of the contest and wasn't there before hand. Thus stories with this (*) will not affect the total number of monster mare stories in that race category for judging.

5941821 the ones from LoveCraft
https://www.google.ca/search?q=lovecraftian&source=lnms&tbm=isch&sa=X&sqi=2&ved=0ahUKEwjc06zDpfHTAhVGKCYKHa6GCnAQ_AUIBigB&biw=1147&bih=618#tbm=isch&q=lovecraft+monsters&imgrc=6MUjdlWcWG7HQM:

This thread has received a much needed update. However, while I still have a lot of work to do, I am also very tired.

Remember if you know of a story with a monster mare that isn't on this list (and isn't NSFW), please tell us the species of monster mare and a link to the story and I will try to add it to this thread.

6797035
Beached has a shark pone in it

6858330 Thank you for showing me this. I will add it to the list.

6858606
youy are welcome

Behold... another update.

Please feel free to mention stories that aren't on this list. If you do, don't forget to mention the race of the monster mare in the story as well. Thank you.

My entry for the 1st Monster Mare story contest, Schneller Geist: The Demon of Hollow Shades, isn't on the list yet. It features the good ol' Maryland / DC area monster / cryptid known as the Snallygaster

6894808 Thank you. It should be added now.

5941821
no tentacle ponies?

6917531 Sadly there aren't any SFW stories of monster mares with tentacles outside of the two examples I gave you. Though if someone were to write one (or even find one), I would love to add it to the list.

5941821
My this is a rather expansive list huh?, thank you for all the hard work.

6944338 Thank you. I worked really hard on it and I try to continue expanding it when new stories are discovered.

The list has received another update.