A Bookworm appears in the Sixth story arc, eating the book of Golden Oaks Library and giving life to fictional characters via magical cocoons and growing in size, but at the end of the arc its discovered that the bookworm was just enjoying the reading not realizing the damage was doing, at the end he helps the main six and Ponyville.
Cats are the inhabitants of 'Wuvy-Dovey Land', and were used as a source of love by Queen Chrysalis when she crash landed in their town.
She and some of her changelings land in the center of a town inhabited by the cats, who immediantly shower them with cakes and love. Although she survives the fall, she and her army are weakened, so they feed off the cats' love and transform their town into the Changeling Kingdom. Chrysalis later harms one of the cats in front of Apple Bloom, Sweetie Belle and Scootaloo. Its fate is unknown.
A cave troll named Jim (after Jim Miller, FiM's storyboard supervisor) appears in The Return of Queen Chrysalis. Chrysalis regards them as idiots.
The six find and enter a cave in the Appaloosan Mountains, where they run into a cave troll, and Twilight Sparkle asserts that it's much larger than the "Cave Dweller's Reference Guide" says that species is. The troll picks up Fluttershy, and brushes her mane with a branch, eventually setting her down on a shelf containing what looks like a giant stone Magic 8-Ball and Optimus Prime.
He grabs Rainbow Dash next, dolling her up, much to Applejack's amusement and Rainbow's annoyance. Rarity then comes up with an idea, and asks Pinkie Pie for help. The idea turns out to be rock and wood replicas of the main six. The troll grabs the Rarity doll and states that he will call it George, much to her horror.
When the ponies are trapped by spiders, Pinkie returns with Jim, whom she has convinced of there being a teddy bear where the other ponies are. The troll sees the spider and is convinced that's the teddy bear, so he drags the spider off, naming him Fluffy.
Chupacabras inhabit somewhere beyond the Appaloosan Mountains. They are the natural enemies of Jackalope. They are based off the Mexican/North American cryptid, Chupacabra.
In The Return of Queen Chrysalis, Fluttershy and Twilight fall down a hole, but Twilight is able to use her magic to get the both of them out of the hole, and once they're out, they spot a Chupacabra. Twilight observes that they only eat goats, but then she and Fluttershy realize the twigs lodged in their manes look like goat horns, and so the Chupacabra begins to chase them.
The others, who are running from the Jackalope, crash into the pair, causing the whole group to tumble down a cliff. Twilight hopes that such a death-defying fall might keep their pursuers at bay. It is at this point that Fluttershy reveals the bunnies' species to be Vampiric Jackalope, as she mentions that they are natural enemies of the Chupacabra, and will fight with it for dominance, and the right to eat the ponies.
They then engage in a fight which horrifies the ponies, with the exception of Fluttershy, who only remarks that nature is fascinating.
Giant Spiders appear in The Return of Queen Chrysalis attacking the main six, but they are defeated by them after Pinkie Pie atracts the attention of the Cave Troll making him believe that the lead Spider is a teddy bear.
A kelpie named Cassie appears in comic|23 as a primary antagonist. She uses her singing to control the minds of ponies and compel the citizens of Ponyville to destroy a dam near the town. To Angel horror, Cassie aims to flood the town. However, she only wishes to do so for the benefit of the water sprites, who cannot reach the ocean unless a path of water is prepared near Ponyville.
In Scottish mythology, a kelpie is an equine water spirit associated with drownings.
Mermares appears in My Little Pirate: Friendship Ahoy!, attacking the Salty Mare, the main six and Hoofbeard discuss with the Mermares but Fluttershy stop the fight showing that sea and earth can love too. A notable member of the Mermares is Jewel who is in love with Hoofbeard.
Imp a Mimicker appears in the Cutie Mark Crusaders Micro-series, she becomes in the comic a new CMC member, the crusaders had fun with her ability to mimic thing, but when they discover she's becoming exhausted they decided to return her to her cave.
The Mightmare Forces corrupted Princess Luna, turning her into Nightmare Moon. When she was cleansed of them by the Elements of Harmony, she assumed them destroyed.
They later returned, and corrupted Rarity, after that they captured the main six and Spike, but they are able to find a way to return them again in Moon Creatures and destroy the nightmare energy. The Forces are led by Shadowfright.
Pinkie Pie and Rainbow Dash happen upon a group of rabbits with horns. One bites into Pinkie's left hind leg, freaking Rainbow Dash out, but only causing Pinkie to give that one the name "bitey". Rainbow Dash picks up Pinkie by the tail and starts to fly out of there, when Rarity and Applejack crash into the two. Applejack uses one of the flowers chasing her to take out some of the bunnies, and the group continues to run again. The flowers do not seem to partake in the chase.
They then bump into Twilight and Fluttershy (running from the Chupacabra), causing the whole group to tumble down a cliff. Twilight hopes that such a death-defying fall might keep their pursuers at bay. It is at this point that Fluttershy reveals the bunnies' species to be Vampiric Jackalope, as she mentions that they are natural enemies of the Chupacabra, and will fight with it for dominance, and the right to eat the ponies. They then engage in a fight which disgusts/horrifies the ponies, with the exception of Fluttershy, who only remarks that nature is fascinating.