Past Sins: Do not hurt Nyx, physically or psychologically, or Twilight will demonstrate exactly why she is Celestia's protege. She'll even go so far as to attack Celestia herself if she thinks it necessary, though there are limits to even the Mama Bear power-up so fortunately nothing much comes of it.
Reality Checks Nyxverse: Twilight, once more. She absolutely FLIPS when Nyx is threatened and nearly killed in Nightmare Night and Nyx. She's only stopped from committing murder by Celestia showing that Nyx was still alive.
Celestia shows a bit of this in Alicornundrum when she threatens Lord Blueblood.
Celestia:DID YOU IMAGINE FOR A SECOND THAT I WOULD REFRAIN FROM BRINGING MY FULL POWER AND WRATH TO BEAR AGAINST ANYONE WHO TRIED SUCH A THING WITH MY MOST BELOVED STUDENT?
Twilight Velvet finally gets her Sparkle Clan brand moment of awesomeness in this manner in the same fic.
Velvet: You won't have to worry about what Celestia will do to you because the last thing you will see in this world will be me taking a bite out of your still-beating hearts. Oh, and don't think I won't do it. My grandson is a dragon. I know how to get rid of the bodies.
The Dark World version of her also qualifies. She kept going for a thousand years of none stop pain and suffering to keep her end of Discord's bargain to turn Dinky back (Discord turned her into a muffin). When the redeemed Twilight, Applejack, and Rarity rescue her along with Spike, she joins them to reunite the Elements so she can uncurse Dinky, being revealed as an awakened Element of Loyalty due to her loyalty to her daughter.
Rarity goes Mama Bear when her baby sister Sweetie Belle is threatened. She even fights Cheerilee The Dragon to Princess Gaia, one-on-one and her zeal is enough to put them on equal hooves. Her rage was great enough that she almost killed Cheerilee if the others hadn't reminded her that Cheerilee was Brainwashed and Crazy at the time and they had to be careful.
G1 Mimic's Dying Moment of Awesome is one of the most popular moments in the entire fic, due to the fact she managed to bust out Discord's tooth, becoming the only mortal pony to ever truly hurt him. We find out in "Origins" that she did it to protect Celestia and Luna, who were her daughters. It didn't help Discord essentually just emotionally curbstompped Celestia For the Evulz. The moment is preceeded by this Badass Boast:
Mimic: You float one inch towards my daughters I will kill you and seal your spirit in one of my horseshoes!
Exploited by Discord with his earthly mother Shady. He knows she loves him, and thus powers her up with an Element of Chaos, allowing her to be his loyal The Dragon and bodyguard, safe in the knowledge she loves him too much to let anything happen to him. Unfortunately for him, he didn't realize she might love him enough to realize he'd gone too far and had to be stopped.
Ditzy Doo gets another dose of this in the My Little Pony: Friendship Is Magic fanfic Shipping and Handling, although since it's a shipping/comedy fic rather than an adventure story, both the trigger and the flipout are relatively tame (but we dread to think what would happen if her daughter Dinky was seriously threatened). She relatively meekly endures a verbal beatdown by the unicorn Glow, who's kind of a bitch, until Glow insults Dinky. At this point, Ditzy a) goes berserk, b) throws a serving pan at Glow's head, and c) tells her where to stick it.
You can insult my eyes, my intelligence, and my disposition all you want, but I will NOT tolerate unkind words about my daughter! Now take it back, you overbearing, self-centered mule!
Derpy has another prominent moment of this is The Party Never Ended, where she uses thoughts about Dinky to motivate herself to help fend off the storm.
And another one in Ace Combat The Equestrian War. When the griffins raid Ponyville in chapter 4 to kidnap fillies and Dinky is taken, Derpy doesn't hesitate to fight three griffins all by herself.
Princess Celestia in Progress and spin-offs will ever so calmly, politely, and nightmarishly deal with you if you threaten her sister Luna.
Six Brides For Two Sisters: Cadence was like this to Twilight Sparkle when they were younger. An older, unfamiliar colt is walking away with the filly you're foalsitting with promises of fun and candy? Poor ShiningArmor never saw the Groin Attack coming. (Fortunately for Cadence and Shining's future romance, explanations and apologies were made afterward.)
In Nosflutteratu, when Twilight Sparkle discovers Fluttershy is a vampire she naturally winds up pouring over her books for any information she can find on the subject. Rainbow Dash drops by just as Twilight is reading about methods to dispose of a vampire. Rainbow reacts...poorly.
In What Have You Done, after Twilight had been kicked out of the CanterlotWedding the only pony who acknowledges her absence is Twilight's mom, Twilight Velvet. When she can't find her in the library and when her friends don't know where she is, Velvet runs out of the reception only to be stopped by Princess Celestia. Velvet attempts to be respectful while trying to leave and look for Twilight, until Celestia keeps blocking her, and trying to reassure her claiming to know Twilight as well as she does. Velvet snaps, and tells Celestia that 1) You are the ruler of Equestria, but you are not Twilight's mother and 2)back off :
Princess Celestia:“Twilight Velvet. Your daughter is fine. I assure you. I know my student just as well as you know your daughter and we both know that she’s-“
Twilight Velvet:“Most definitely not fine.”
Twilight Velvet: “I do ever so apologize, Princess, but I must correct you on one little thing. Twilight may be your student, but she is my daughter. And she will always be my daughter. I know Twilight. I’ve known her for far longer than you have, and I know her far better than you ever can, because there are things she would never bare to you. I know her pain, I know her fears, things that you could never understand, because you are a goddess. A being above us. And I respect that. I honor you as my ruler, but I will never honor you as my sister, or as a fellow mother. Now, move aside, so I can save the mare that you helped break.”
And Celestia does. Even the guards were amazed.
Mirrors Image: Chrysalis. When her last daughter died from emotional neglect, she made sure the ponies who were supposed to be raising her went to prison, and stayed there. Plus, there's the whole "invading Canterlot to recover her daughter" thing.
Her mother, Queen Amethyst, was a Knight Templar Parent and a Jerkass, but she still went after Celestia for breaking her daughter's heart. And she won.
In the Lord of the Rings fanfic Ancient Prophecy fullfilled, one of the Valar (the gods without Capital G) slew the children of their Guardians. Understandably the Guardians in question weren't so thrilled. They battled the Fourteen Valar, destroyed the city they dwelled in and still inspire such fear that the Valar have to call upon the in that fanfic formerBig Bad to aid them!
Karofsky's mom in the Glee fanfic The Kurtofsky I Ms. There's a reason she demands to be called Mrs. Badass and the reason is that she beat up Azimio with a golf club when he tried to destroy Karofsky's car.
Mary Jane Watson is an unusual variant in that she's a Daughter Bear. She currently has much better control over her emotions than she did when she first became a superheroine, but threatening her family and close friends is still her Berserk Button and anyone who threatens them will suffer.
In Harmony In Disarray, Alex Russo is this towards Leigh as she once broke Galloway's nose (and her own hand!) when he pushed Leigh, and before that she was already one as far back as the beginning of the story.
Every female character with a child in The Legend of Spyro: A New Dawn and its sequels, even the Big Bad Deadlock. Given most of them are female Dragons, it seems it's just a natural trait for them to have. Cynder takes it up a notch, due to her own horrific childhood making her want to protect her child from suffering the same thing. The only subversion is Queen Gorgon, the Queen of the Naga that Deadlock overthrew.
In the Axis Powers Hetalia fanfiction The Howl of the Wind, the spirit of the personification of Native America returns to torment the various nation for raping America. While haunting France in his sleep, she actually turns herself into a bear and starts clawing him to pieces.
In Broken Bow, do not ever, EVER, attempt to harm, marry, or hide Armani Dove within the vicinity of Artemis, if you don't want to be attacked with so much force, that Athena thinks it could even destroy Zeus. It doesn't matter if you're Aphrodite, a clueless nymph, or even her own Brother... just don't.
In turn, Marisa's mother figure, Mima, is terribly protective of her. Marisa tends to get uncomfortable when Mima voices her concerns regarding the witch's mortality, and how to solve that little "problem". Of course, this doesn't stop Marisa from using it to coerce Mima into Yukari's god-killing hit squad.
In Eva Sessions: You Can Never Trust, a character is being real obnoxious to Asuka, getting rudely into her personal space — in spite of her telling him she wants him staying away her and not talking to her — to insult her and deliver her a (pretty hypocrital) "The Reason You Suck" Speech, when Eva-02 suddenly roars and tries grabbing him. The boy bolts out of the place instantly, utterly terrified and realizing he has soiled himself. Although nobody else understands why the Humongous Mecha has done that, but Asuka notes that it was protecting her. This is because Asuka's mother's soul is stuck inside her robot. And Kyoko wants you leaving her daughter alone.
In Heir of Prince Harry turned out to be the long-lost son of Snape and Bellatrix Lestrange. This tidbit sent the other Death Eaters into a panic because, in Lucius Malfoy's opinion, "The dark lord was scary, but Bella in overprotective mother mode was lethal. He was slightly more afraid of Bella than he was of the dark lord."
In the Rise of the Guardians fic Guardian of Light, the main character, Helen Bennett, is taken by Pitch. While the Guardians do show up to rescue her, they're not the first to show up; the first to show up is her adoptive mother, Bernadette Bennett, in a tag-team with her ex-husband. She's armed with only a baseball bat, which leads to one of the biggest Crowning Moments of Awesome in the entire story, complete with an awesome shout-out.
Bernadette: Get away from her...PITCH!(whacks him with baseball bat)
Not to mention it's a Meaningful Name; 'Bernadette' means 'brave as a bear'.
Helen's biological mother, Charisse, died protecting the newborn Helen from Pitch (along with Helen's elder sister, Eartha).
By the same author above, there's the Megamind & Rise of the Guardians crossover fic Protectors. Megamind (known as Teal in this fic) has been adopted by the Warden and his wife, Andrea. Said wife gets to the stage where the Warden is unsure whether or not to comfort her...or to remove any objects within her reach which could potentially become a weapon.
And when she comes face to face with the two who attempted to manipulate her adoptive son into becoming a villain:
Andrea: "Since you two obviously make poor parents, you don't comprehend how angry I am. So I'll give you a hint." (punches them both) "Try doing that to my son again, and I'll make you wish for something as sweet as pain."
The most violent is Khan's lover, Victoria, who was ready to level Starfleet when she woke up and discovered that her unborn child was gone. She then becomes this to her new surrogate daughter, Lucille, and breaks Dr. Korby's arm after he kidnaps the girl.
Lucille's biological mother gets a moment when she dies fighting Korby upon realizing the man harmed her.
Uhura is this towards her unborn child. When Korby tells her that he intends to inject the baby with Khan's augmented blood (which could kill it), and that having her child would be useful since the baby is part Vulcan, she leaps at him in rage.
Kirk's mother, Winona, gets an awesome moment in the first chapter. After the events of the movie she arrives in the holding room where Khan is with McCoy, and tells McCoy to leave. He does, quickly. Remaining calm the whole time, Winona then punches Khan so hard herolls backwards off the bed. And then, after she dishes out her threat, she just turns and walks away.
Winona: Do you happen to know what a mother bear does to anyone who harms her cubs?
Khan: I do.
Winona: So you probably have a good idea of how I'm feeling. (punches him in the face, and then calmly walks over to where he's landed) I would kill you now, but you may still be needed to save my son, so I won't. But that doesn't mean the thought has left my mind; I'm only going to say this once, and I'm going to make it very clear. If you hurt or threaten my son again, I'll come after you. I won't need Starfleet, or a Vulcan; hell, I won't even need a Klingon Empire. I'll come after you, and when I find you, I'll blast a hole straight through your cold heart. Then I'll cut off your head, and you arms, and your legs; you'll be in six pieces, and I'll bury a piece in one. Continent. Each.
McCoy's ex-wife, Pamela, could be a darker, Ax-Crazy example. She shot and killed several security officers while defending Joanna before said daughter was forced to stun her.
In the Soul Eater fanfic In Fever Dreams, Maka's mother is a literal Mama Bear, being a bear witch and all. The first scene of the fic has her clawing a Kishin egg to death for going after eight-year-old Maka.
Harley: (advancing on Joker with the hammer) You filthy scum sucking CREEP! You lousy, good for nothing, son of a weasel! You hurt him!
Joker: Now, Harley...I can explain!
Harley: Go on! Try it! I dare you! (hits Joker in the stomach with the hammer, then grabs him by the shirt and pulls him up to her face) I love you, Puddin', but you stab my baby again and even Batman'll feel sorry for you! Got it?
Though not exactly Keitaro's mother, Haruka fits the bill in chapter 6 of Contract Labor; when Naru tries to attack Keitaro after an Accidental Pervert moment, Haruka physically restrains her, threatens her with a pocketknife, and explicitly threatens to use said knife on Naru if she doesn't back off.
In No Hurry At All Mrs. Weasley went ballistic when Dumbledore expressed his disappointment at Death Eaters having been killed during a fight in which most of the family participated.
You listen to me you old goat. If the price of my children being safe was to behead every single one of those murdering bastards, I would take up my meat cleaver and do it without one ounce of remorse. If my children are in danger, the Death Eaters are going down hard.
Inuzuka Tsume, Konoha Town's police chief in Kitsune no Ken: Fist of the Fox, is this for her son Kiba. Her first response to news that Kiba may be in trouble is to send dozens of cops to the location to arrest whoever's responsible. There's also her threat to Naruto following his confrontation with Kiba (for which Tsume had sent out the aforementioned cop-squad):
Tsume: If my son ever got so much as a scrape on him from you, I don't care if you were part of a group that terrified whole cities, I would stuff a shotgun up your ass and pull the trigger. Am I understood?
Naruto:(meekly) Yes, ma'am.
In Gensokyo 20 XX, try to use and manipulate Yukari's love for the children she cares to get her to kill them, try it and you'll find you won't succeed because, mentally ill or otherwise, Yukari will try to kill you. Seija learned the hard way.
A pregnant Ran is a more downplayed example in Life in Gensokyo Village in chapter 10 but we clearly know she is a force to be reckoned with, stating that if Yukari and Reimu's birth-mother were to quarrel over who can have Reimu that she was to take Chen and Reimu and stay somewhere else.
Joanne DeSoto in thisEmergency! fic. She loves John Gage like another of her kids, and when someone tries to attack John to get revenge on Roy, who he blames for,his brother's death, Joanne stops him with a tire iron to the head.
Pidgeot in A New Chance Series is very protective of Ash, a year away from him hasn't diminished that, and being the leader of her own flock has accentuated that feeling. When the Fearow near Pallet Town tries to kill Ash, she goes berserk and knocks him out the sky in one blow. The she flies over to Ash and gives him a big hug.