Brought Down To Bad Ass: During Discord's relapse, Twilight fought him as an alicorn and indirectly nearly caused Fluttershy's death. She then depowered herself afterward out of guilt and due to viewing herself as unworthy of such power.
Power Copying: Twilight is able to figure out how to cast spells by seeing them performed.
Power Limiter: Twilight had her alicorn powers sealed and princesshood abdicated after a moment of recklessness harmed Fluttershy, thus explaining why she's still a unicorn. She reclaims it during her fight with Nightmare Brutality.
Crazy-Prepared: According to the Mann Co robots. Their analysis is that Pinkie is either capable of breaking the laws of physics, or she's prepared for any scenario, up to and including dueling with a magical knife-wielding psychopath. Canonically, she could be either, or both.
Handicapped Badass: After Rainbow Dash is temporarily blinded, Sniper trains her to use her other senses to see. She is able to detect Twilight from the sheer feeling of her magic, whereas she identifies Rarity by her perfume overuse.
Oh, No... Not Again!: Rainbow Dash has apparently ended up in one of Hugh Jelly's "personal use" vats of jelly before.
An Arm and a Leg: She loses one of her legs when she rescues Gem Sentry from Nightmare Clockwork.
And I Must Scream: When Rarity is brainwashed by Nightmare Cuddles, he leaves enough of her intact that she knows what she's doing and can't stop it.
Bi the Way:Applejack and her used to date. It ended because of their clashing personalities.
Every Device Is A Swiss Army Knife: Rarity's artificial leg also functions as a hand, a gem cutter, a flashlight, a drill, pickaxe, shovel, wrench, lightning gun, and diamond - tipped chainsaw.
Extreme Omnivore: Rarity is a mild version. As she puts it, her mother's horrible cooking is the reason why she has a greater poison resistance than that of a dragon.
Mad Oracle: Because they both bear elements of Generosity, when Engineer is turned into a Nightmare, Rarity knows what's happening to him. She's not able to convey the news very coherently, though, as she's seeing what he's gone through.
Scars Are Forever: Because the wound was caused by a Smooze creature, Medic can't regrow Rarity's leg. Engineer and the Doctor construct a replacement, though.
Took a Level in Badass: Like Trixie, Rarity has also seen the need to improve, learning to teleport among other things.
You Are Better Than You Think You Are: Fluttershy freaks out over the thought of fighting the changelings in order to rescue BLU Soldier, Doctor Whooves, Derpy, Spy, and Sparkler. BLU Heavy tells her she can find her own strength in kindness.
Ascended Extra: Although she was never truly an extra in the traditional sense, she has her role greatly extended from the TV Show as the Element of Hope.
Big Damn Heroes: She shows up just in time to interrupt a possessed Twilight.
Bully Hunter: Trixie makes a habit of ruining the Flim Flam brothers' scams whenever she can, almost solely for her own amusement.
Loophole Abuse: Trixie pulls this on Flim and Flam to render their victory over the Apples moot. They really want the Zap Apple grove, but since the grove is technically part of the Everfree Forest and not the Acres, it's under custody of Ponyville and the Mayor, and she's perfectly willing to lease it to the Apples. When they think they can at least make money off the farm proper, they are informed in no uncertain terms that nopony will do business with them, all the other Apple families in Equestria will boycott them, and Rainbow Dash is within her rights to deny them the rain they'd need to grow anything in the first place.
Took a Level in Badass: Trixie took the opportunity to beef up her magic skills (without evil amulets this time) before returning to Ponyville for the third time so she could live up to her title.
Ascended Extra: Although she was never truly an extra in the traditional sense, she has her role greatly extended from the TV Show as the Element of Trust.
Batman Gambit: Zecora, as Spycora pulls off one of these against Nightmare Clockwork. In order to get past a corridor filled with death traps, she uses some magic dust (a Zecora trait) to create a smokescreen to hide, knowing that Clockwork would most likely panic and fire off all the traps. True enough, Clockwork does indeed fire off all the traps, only to find that Spycora didn't move at all, and simply walks past all the traps as they reset. And then, just to rub it in, she lights a cigarette off of some smoldering flames left by a laser beam trap.
Sympathy for the Devil: Derpy learns that the changelings need to eat to survive, just like everypony else; the problem is that that their hunger for love affects other ponies. With the help of BLU Soldier and Cadence, she creates a self-renewing source of love so the changelings won't ever have to hunt for love again. This prompts Chrysalis' Heel-Face Turn.
Authority Equals Asskicking: Curbstomps a mind-controlled Barricade for picking a fight with her, and makes Spike (who was also mind-controlled and turned into a huge dragon) learn the hard way why dragons don't attack Equestria anymore.
Bad Dreams: Which was Slenderman's doing, which directly caused the BLU team to be brought to Equestria.
Fake Memories: Luna does this to everyone in Ponyville but the BL Us and the bearers of the Elements in the aftermath of Nightmare Grave's attack on Ponyville so they don't remember all the Nightmare Fuel they experienced. They instead remember a Lighter and Softer version of events.
Living Lie Detector: Spy tries a hastily made cover story against Celestia and Luna. As she once bore the Element of Honesty in the Waking Nightmares timeline, Luna retains some of its power, and thus is not fooled.
The Resenter: Towards Celestia in the past, just like in the show. This led to her corruption by the Smooze
Burning with Anger: Her mane and tail turn into flaming coronas when she learns Grey Hoof turned everypony into zombies.
Earlier, she also does this after learning Sunnytown murders anyone who has a Cutie Mark, foals included.
Drowning My Sorrows: Celestia did this for fifty years out of guilt for what she did to Luna, and because of that she approved of laws she shouldn't have. She is currently trying to get rid of said laws.
Hurl It into the Sun: Celestia inverts this trope by summoning a small sun in the midst of the Daleks.
My Greatest Failure: Celestia views banishing Luna to the moon as this, since it showed how inattentive she was to her little sister's resentment and envy of her popularity with their subjects, which ultimately led to Luna's corruption into Nightmare Moon in the canon show.
Omniglot: Princess Celestia learned every language a long time ago. Justified in that she's certainly had time.
Reassigned to Antarctica: According to Word of God's tumblr, Shining Armor did this to Flash Sentry because he is a sexual predator who wanted bragging rights for having slept with an alicorn. When this came to light, Shining had a "long, civilized talk" with Flash before reassigning him to the farthest military outpost in the Frozen North.
Eaten Alive: The grisly fate of Nightmare Gardener. Having her body consist of a mass of extremely poisonous flowers was a good idea - less so when changelings are immune to it and consider it to be delicious candy.
Heel-Face Turn: Chrysalis did this after learning Slendermane strung her around For the Evulz. That and she and the changelings were given an artificial self-renewing source of love by Derpy, Soldier, and Cadance, removing the need to hunt for food.
Mama Bear: Queen Chrysalis, after her Heel-Face Turn, would rather engage a Nightmare on her own than let her children get killed. Having a psychic bond that lets her experience their deaths may be a strong motivator.
No Sell: Being the embodiment of chaos allows Discord to shrug off Slendermane's powers and illusions, since he's already mad to begin with.
Sealed Evil in a Can: About a year after 'Keep Calm and Flutter On', Discord relapsed and tried to take out Celestia, hurting Fluttershy in the process. Once he realized what he had done, he surrendered and willing went back into his can.
Scout: "I'm not sure I wanna see where this fanfic goes next..."
Dark and Troubled Past: When Scout was younger, a French-Canadian wearing a rainbow shirt broke into his home and tried to rape his mother before his eyes, even threatening to kill him as a bonus. To save her, Scout beat the man to death with a baseball bat. The incident traumatized him ever since.
Parting Words Regret: Soldier/Solomon got into a fight with his brother, Lucas, who wanted to enlist in WWII. The fight makes his newborn daughters cry and he leaves on an errand, only for the infamous attack on Pearl Harbor to begin. His brother and entire family was killed when a shot-down plane crashes into his house.
Roaring Rampage of Revenge: The deaths of his family drove him insane and thirsty for revenge, and he wanted to kill those responsible. This led to his Nazi-killing rampage in Europe in Team Fortress 2.
Abusive Parents: Pyro's mother. In Chapter 30, it's revealed she made her own daughter work as a Sex Slave, and was responsible for most of Pyro's burns. Pyro eventually burned her to death in retaliation.
Berserk Button: Insulting Engineer around Pyro is a very bad idea. Hurting Engineer and having her find out about it is pretty much asking for an instantaneous incineration.
True Beauty Is on the Inside: In her original human form, Pyro is a pudgy mess of scars and burns due to her pyromania and abusive childhood, but Engineer says that she's an angel on the inside - in contrast to his ex-wife Irene, a monstrous harpy of a bitch with the body of a superstar photo model. The scars were omitted when she crossed over into Equestria, though - as a pony, Pyro is very pretty.
Fusion Dance: With Applejack. This makes BLU Scout provide his own theory on the trope. Naturally, they aren't pleased with him.
Didn't Think This Through: As Nightmare Cuddles leaves Rainbow Dash and Sniper after using his hypno eyes on them, he realizes that he forgot that Rainbow was currently blind, thus protecting her from the hypnosis.
Foe-Tossing Charge: Heavy barrels through several corrupted Diamond Dogs to get to Fluttershy.
Mind Rape: Heavy's ability as Nightmare Cuddles. His repertoire ranges from just making you happy and lazy, to removing your memories and adding subconscious orders, to trapping you in a delusion while a small part of you in unaffected and forced to watch.
Your Approval Fills Me with Shame: In Heavy's backstory, he was beaten by his old commander for showing compassion to a dead sparrow. When he killed him years later out of revenge, the man approved of his actions, leaving Heavy without any satisfaction in doing the deed.
The Atoner: Engineer really feels bad about the things he did as Nightmare Clockwork, including Rarity losing one of her legs.
Oblivious to Love: Does not know about BLU Heavy's attraction to him. Given Medic's past, it may be for the best.
Papa Wolf: Do anything to his friends and he'll think up various ways to ensure a painful death. And he has a vivid imagination.
Super Mode: Medic's Übercharge in regards to the Elements of Harmony. Using it on them temporarily turns them into an alicorn.
The Atoner: He collaborated with the Nazis as their spy in return for the survival of his village, but they later betrayed him by occupying his village and raping his mother to death. He killed every Nazi there and considered committing suicide, but then he heard of Soldier's rampage in Europe and secretly fed him information in an attempt to redeem himself.
The Casanova: Spy seduces the ladies with astounding ease. Even the pony ladies. Medic warns Spike not to mess with Spy over the fact that he's living with Rarity, as he may decide to woo her out of sheer spite. On the other hand, he claims to have had genuine feelings for many past conquests, including Scout's mother.
Cigarette of Anxiety: Spy badly needs one after seeing Discord's reign, before Celestia and Luna intervened.
Dope Slap: Spy does this to Scout whenever he gets fed up with him.
Scout: "That hurts more with hooves, y'know."
Flat "What.": Spy does this after hearing Soldier's plan before their first battle, which is completely unintelligible because of him using a bunch of gibberish code phrases.
Innocently Insensitive: Spy used to tease Scout all the time about his fear of rainbows and dating his mom, never knowing that Scout's Berserk Button originated from his mom nearly getting raped. When he does hear the truth, Spy immediately regrets picking on him.
Summon Bigger Fish: During Pony Versus Machine, RED Scout realizes they only have one option to deal with the Freaks — bring out their own. Painis Cupcake nearly kills Scout before he sets his target on the bigger and tastier opponents.
Determinator: Despite facing an unstoppable Eldritch Abomination with no chance of survival, RED Medic absolutely refuses to let Slenderman take RED Heavy, desperately firing Heavy's minigun, Sasha, at the foe. His conviction is so great that he manifests the Dark Crown of Magic and empowers Sasha with Harmony, which is one of the few things capable of actually injuring Slenderman.
For Science!: Medic's answer for keeping BLU Spy's head in his fridge.
Papa Wolf: In Chapter 15, he protects a comatose RED Heavy from an avatar of Slenderman by tapping into the Elements of Magic and Kindness through Sasha. Doubles as a CMOA
Flat "What.": Spy does this when he realizes why Soldier created the Decoy MvM map.
Twin Threesome Fantasy: Suggests this option after crossing over to Zecora, who against her better judgement actually entertains the possibility. They actually do it by the time of "Running of the Leaves".
Groin Attack: Gets subjected to a few of this after insulting the RED team one too many times.
Heel-Face Turn: Does this after he grew tired of keeping secrets from the RED team, including Soldier.
Manipulative Bitch: In Chapter 15 it's revealed that years ago she tricked Merasmus into giving her a spell that splits a person's soul into two halves. This is how RED and BLU were created from the original mercenaries.
And sometime after that, she made RED Demoman and BLU Soldier, who were close friends, hate each other by making them believe the other one betrayed him, solely on the basis that people from enemy teams can't be friends.
Mitta: "If either want (sic) to protect every pony in Ponyville from suffering a Fate Worse than Death, then you have to come with me at once."
It's All My Fault: She feels VERY MUCH responsible for the death of her younger sister Ruby.
My Greatest Failure: Mitta failed to save Ruby from being killed by Sunnytown's residents for possessing a Cutie Mark.
No Sell: Mare-Do-Well's mask shields Mitta from Smooze spit, allowing her to simply shrug it off.
Redemption Equals Life: Celestia turns her into a living, breathing pony again, both as a reward for her role in defeating Grey Hoof, and as an apology for turning her into a zombie despite her innocence.
Set Right What Once Went Wrong: Inverted. When Mitta, Demoman, and Applejack are reliving a traumatic event in Mitta's past, she needs to proceed through the memory as it really happened, letting her sister die to snap the others out of it.
Grey Hoof (aka Nightmare Grave
And I Must Scream: His ultimate punishment: Celestia imprisons him in the ruins of Sunnytown, and places a geass on the village to turn away forms of life from Sunnytown's former location, as Sunnytown has also shifted dimensions so that he can't be seen by anyone else. And to add insult to injury, Celesita's spell also prevents Grey Hoof from going insane.Proof that you should neverpiss Celestia off.
Body Horror: Grey Hoof'svery disturbing Transformation Sequence. His skeleton, and only his skeleton, grow to the size of an alicorn. He also grows bone wings and a horn. As expected, this tears his flesh apart.
Bored With Insanity: Grey Hoof and his buddies were insane for part of the time they spent as cursed zombies in Sunnytown. Eventually, they got better.
Deal with the Devil: Grey Hoof does this with Masky Pegasus to gain freedom for him and his friends after Celestia cursed Sunnytown to live as zombies as punishment for their actions. However, once his friends learn the price for their freedom, they immediately Heel-Face Turn and abandon Grey Hoof out of disgust.
The Worf Effect: The biggest and physically strongest of the Captains. She goes out of her way to avoid this (and even lampshades it at one point), but it can't be helped at times due to the power level of the villains everypony's been facing.
Shrinking Violet: He's a nervous, easily frightened thing, just like his daughter Fluttershy. When someone's hurt, however, he becomes completely fearless in treating his patients. Plus, he absolutely detests Harbinger.
Big "WHAT?!": He corrupts BLU Heavy into a Nightmare form, but unlike previous Nightmares, BLU Heavy turns into an alicorn-sized plush toy named "Nightmare Cuddles". It's not something it or anypony else expects.
Oh Crap: Masky Unicorn's eyes widen when Medic's ÜberCharge turns Applejack into an alicorn and uses the power of truth to cure Spy and the princess's guards from their corruption. Then it gets a good look at the princesses, and decides to run.