Armitage III, Dual Matrix. The entire movie is Naomi Armitage having one giant Mama Bear moment (And her partner and lover Ross Sylibus makes an impressive Papa Wolf to back her up). To really drive home just how far Armitage goes with this: she gets hammered up and down by various 'bots and things unto being torn apart multiple times, her daughter Yoko discovers her mother is a robot by seeing her metal skeleton through a cut-wide-open shoulder and reacts with the prejudicial horror any child in that universe would feel, jerking away from Armitage and hiding behind Ross after Armitage has been badly injured by two clones of her with razor blades on murder-skates. Armitage swallows her tears, turns and goes to fight the clones again, knowing it's a fight she almost certainly can't win. At the end of the film, one of the clones is holding Yoko by the throat. Armitage, beaten and weary unto near unconsciousness, staggers up behind the thing and manages to grip its shoulder, and utters a line that exemplifies this trope.
After having been through a very horrific ordeal during the Great Eclipse that ended with her going completely insane, Casca has the mentality of a 2-year-old child and can't take care of herself. Right after the Eclipse, she miscarries the baby she was pregnant with due to the extreme trauma that she suffered but it turns out to be tainted with evil as a result of what Griffith, in his newly-incarnated demonic form of Femto, did to her. Guts, the father of the child who is there, immediately tries to kill it, but Casca, through a surprising act of maternal instinct, tries to protect the child, before it disappears by daybreak. Poor Casca is then left screaming and crying in grief, which leaves even Guts in a moment of despair.
The Child makes several more appearances to its mother in order to protect her. After another series of unfortunate events, the Child makes his first human appearance, which is far less appalling. He has taken a liking to both Casca and Guts, but Casca, in another surprising twist, acts very motherly toward him and is fiercely protective of him, not allowing anyone to touch the Child.
Bitter Virgin. When Hinako's mother realizes that her daughter's (second) pregnancy was the result of rape, and that the rapist is her own second husband, the next time she sees him she chases him out of the house with a knife.
In Black Lagoon...For the love of any deity you believe in, do not harm any of Balalaika's subordinates. If you do, she will hunt. you. down. Some may see that as twisted, but others may see that as what proves she's still human: those men are all she has anymore, so she protects them fiercely and will NOT let any harm to them pass. Proved when she engineers the traps that get Hansel and Gretel ultimately dead, and as Hansel talks to her and then bleeds to death when she has his arm and leg pretty much blown off, she keeps mentioning the reason why she's doing so: to punish the Vampire Twins for blowing up one of her soldiers, then horribly torturing another to death, and then mocking their deaths in front of her.
And Balalaika's quite reasonable and easy to deal with, compared to the Lovelace family Meidos, Rosarita Cisneros aka Roberta and Fabiola Iglesias. If you, the gods forbid, kidnap or harm a Lovelace, either or both of them will come. for. you. Roberta's explicitly compared to the Terminator, and later on shoots her way through a group of US Special Forces, singlehandedly. Fabiola's not quite as formidable as her mentor, but she's still nobody to trifle with, and may be going the same way (if, you know, less psychotic than Roberta).
An interesting example of this trait being applied to a villain comes from Tia Halibel, the third Espada. Unlike most of the arrancars, who love violence and don't give a damn about their comrades and subordinates, Halibel strongly believes in her True Companions and The Power of Friendship, having a very tight bond with her three subordinates. While Halibel doesn't typically fight often or very hard, when her three fraccion are in danger, she goes into a state of Tranquil Fury and shows why she's ranked as the third strongest in Aizen's army. Halibel's aspect of death is Sacrifice because of her willingness to sacrifice herself for her friends, but also because they're equally willing to sacrifice for her.
Ichigo reveals early in the manga that his Missing Mom gave her life to save him from a hollow. Subverted. Masaki was such a powerful Quincy, the hollow was absolutely no threat to her at all and she would have played the trope completely straight for Ichigo. Her power was stolen in the middle of the fight by the Quincy King, rendering her suddenly powerless. Instead of curbstomping the hollow, she was killed by it - while still trying to shield Ichigo despite having lost her powers.
Retsu Unohana's angry stare can terrify even the 11th Division enough to stop bullying her squad. It's revealed she is the progenitor of the 11th Division when she trains her old protegè and rival Zaraki. She fights to the death to make sure Zaraki achieves his potential and it's both terrifying and Creepy Awesome to watch her fight.
Bokurano. Never EVER threaten or bully Kana Ushiro near to Maki Anou. She might not be her relative, but she'll still do her best to drive you away from here.
Teresa of the Faint Smile in Claymore, after adopting Clare, breaks the taboo against killing humans after bandits raid the town where she left the little Clare, and refuses to accept the organization's punishment in order to stay with her.
Clarice ends up being one to Miata, despite the fact that, as the weakest Claymore, anything Miata can't defeat she certainly can't defeat. Nonetheless, she still stands up to protect her.
Rem of Death Note falls under this trope; having sworn to protect Misa after Gelus, another Shinigami, died doing so, she acts as a guardian of sorts and threatens to kill Light if he brings her harm. Eventually he uses her protectiveness against her, and forces her to sacrifice her life to kill L and Watari in order to save Misa.
Ran is known to go Mama Bear for any kid she is in any way in charge of. One episode has a creepy guy who turns out to have been employed by an Italian criminal following the Junior Detective League to try to steal a piece of paper from them. Ran throws a warning punch at him and says that if he doesn't leave them alone, she'll call the police. In another story, it looks like a client of her father's - a high school girl - may have been kidnapped by dangerous people; Ran thinks she sees the kidnapper spying on her place... so she jumps out the window to confront him. When he runs, she chases him down the street and punches out the driver's window of his car, demanding to know where the girl is. He actually wasn't the kidnapper, but it was still pretty awesome.
Subverted in (of all series) Dragon Ball Z. Goku's wife ChiChi is odd in that she's both taken a level in badassand was Overshadowed by Awesome alongside half the case... so she has her limits, but then again, she has her limits. Her Victorious Childhood Friend and husband has been dead for seven years, she's been led to believe that her older son has followed, and ChiChi is absolutely out of her mind with grief. While her father is able to hold her back the first time she tries to attack him, eventually she does walk right up to Super Buu, slaps him, and demands he bring Gohan back. Buu stares at her, turns her into an egg, and promptly crushes her. Worst of all, her seven-year-old son was watching the entire time.
In a filler episode just before the Trunks saga, however, ChiChi gets to play the trope straight. She hires a private tutor for Gohan by the name of Mr. Shu, unaware that he's a cruel Sadist Teacher who repeatedly kicks the dog by calling Goku worthless as a father and makes the poor kid bleed. Then she finds out. It does not end well for Shu.
In two filler episodes during the Namek Saga, there was a Giant Crab that antagonized Bulma, to which Bulma also led her to attack Blueberry and Raspberry later on. It's strongly implied that their being in close proximity to their offspring, and in the case of Blueberry and Raspberry, stealing them under the belief that they were dragonballs, was what resulted in the crab attacking them, as both times the crab attacked, the characters it attacked were near its eggs.
Really, all of the mothers in the series are this in one way or another. ChiChi might be overshadowed, but Goku, Krillin, Piccolo, and pretty much all of the main Z-Fighters are terrified of her, especially when anything involving her children is going on. Bulma has her moments as well, most noticeable when Trunks is training with Goten during the Buu saga. 18 also shows this in GT when her Brainwashed and Crazy brother targets her daughter (after murdering Krillin in front of them both). Really, no matter how Overshadowed by Awesome and Out of Focus many of the female characters are, you do not mess with them or their children.
In Fight! Iczer-One, when the title character and her partner Nagisa are getting their butts kicked in a mecha battle against Iczer-Two, Sayoko (the little girl whom Nagisa met and decided to protect in the previous episode) tries to encourage them. Iczer-Two, in annoyance, responds by stepping on poor Sayoko with her mecha. Nagisa's resulting fury gives her mecha a massive power up, and she and Iczer-One proceed to wipe the floor with their opponents. Afterward, it turns out Sayoko was protected by the bracelet Iczer-One gave Nagisa (who in turn gave it to her), and thus survived.
In Fruits Basket, we have Kyoko Honda, Tohru's mom. She was in a gang before her marriage to Katsuya, and while we never get to see her in action, it's heavily implied that she wouldn't think twice about reverting to her darker days to protect her daughter. Now Tohru's friend Arisa, who greatly admired Kyoko and once was saved by her, steps in to be the Mama Bear; her other friend, Saki, friend is like that too, even more so than Arisa as she scares the SHIT out of the Alpha Bitch and her Girl Posse if they try to bully Tohru when she's near.
When Tohru was a little girl, she once went missing. As Yuki can testify, Kyoko was so worried and upset at how the police couldn't find her daughter that she was seriously about to beat the shit out of a policeman if he didn't find her in time.
Izumi is practically Ed and Al's second mother. She barges into Greed's hideout to rescue Al after taking down one of the homunculus' cronies. Add to that her furious introduction and, well...they learned why it's an extremely bad idea to piss off one of the most Badass characters in the entire story.
An episode of Futari wa Pretty Cure gave Honoka's grandmother a chance to be Grandma Bear. Pretty impressive feat for an non-superpowered elderly woman.
In Gokusen The Rookie Teacher Yankumi is this to Her students, even coins the phrase, "Mess with My Kids I...Will ...Kick ....Your ...ASS!!"
Hajime no Ippo actually featured a very literal Mama Bear that tries to kill Takamura. It doesn't end well...For the bear.
Haré+Guu. Amazingly, (but awesomely) Weda, with the bank robbers
From Hell Teacher Nube, aside of the Teacher Wolf male lead Meisuke Nueno aka Nube...a more traditional Mama Bear example is his co-worker and Ritsuko Takahashi, whose Crowning Moment of Awesome involved fighting a demon alone to protect a student of hers. Notice that Ritsuko had NO powers (unlike Nube), clearly knew she wouldn't be able to win the fight, was grievously injured...and she fought anyway, succesfully holding off the monster until Nube came to her aid.
Izuna eventually becomes one to a "boze" (the soul of an unborn baby that she accidentally misplaced during an exorcism) who then takes refuge in her body (and makes her look really, really pregnant), since they're haunted by a boze-eating monster.
Ishida's mother in Koe No Katachi goes Mama Bear on him when she connects the dots, his oddly cleaned room, his sudden lack of possessions, the ripped in half calender marking down to the day when he without reason left a huge bundle of money by her bedside... and realized her son had been planning to commit suicide. She absolutely rips into him, screaming to high heaven at him for even thinking of doing so and completely freaks out Ishida.
The title character in The Legend Of Mother Sarah is pretty much the epitome of this trope in Japanese media, as the series' title implies. The story is basically about Sarah, a Determined Widow who lost her children Tsurumi and Harato years ago, and is now Walking the Earth to find them again. Needless to say the "reunion" won't be that easy: their "Earth" is a a Mad Max world after a terrorist attack threw it into confusion - so to find the kids, Sarah kicks ass. Hard.
Madlax: What ever you do; DO. NOT. EVER. lay a finger on Margaret. Unless you really like getting the snot kicked out of you by her Ninja Maid Elenore.
Seriously, don't mess with Vivio. In A's, the season before StrikerS, Nanoha loads three cartridges into Raising Heart as a prelude to blasting an Eldrich Abomination that has a habit of destroying entire worlds; just before she lets all hell loose on the poor sap who kidnapped Vivio, she loads five- then slaps in a second clip. The results are satisfyingly explosive.
In Mahou Sensei Negima!, Chizuru slaps a high-ranking Demon when he breaks into their house and attacks Kotaro, whom she has decided to adopt. Although it wasn't really all that effective in the end, the fact that she managed to stop his attack cold is rather impressive for one who is supposed to be an Ordinary High-School Student...
Once they get to the Magic World, there's a literal Mama Bear. As in, a bear-woman that the characters call "Mama". And she will wreck you if you abuse the slave girls (Ako, Natsume, and Akira) she's watching over.
Mawaru-Penguindrum: Chiemi Takakura, like her husband Kenzan, loves and cares very deeply for her kids. In episode 9 she's seen shielding her daughter Himari without hesitation when a huge mirror falls on her; for that, Chiemi sustained severe cuts in her face and arms and had to be hospitalized.
As of 547, we have another one in the form of Gaara's mother Karura. She was determined to protect her son, enough so that dying wasn't enough to stop her. Remember how Gaara said that he believed his sand was commanded by his mother's spirit? It turns out that he was right.
Shinji and Asuka's mothers are locked inside their respective Humongous Mecha. So that, when the Evas go berserker it is actually their pilots' mothers going berserker:
Unit 01 goes berserk whenever Shinji is in trouble? That's actually Yui Ikari.
Youtube comment: Shinji ain't happy, so mama ain't happy. We're all not happy if mama ain't happy.
And what helped Asuka avoid being killed by the JSSDF? The half of her mom Kyouko's soul that remained in Unit 02 after the failed experiment that rendered her insane.
Asuka: Idonwannadie, idonwannadie, I DON'T WANT TO DIE!!!...Mama, you've been here all along?! MAMA! (giant cross of light erupts from the lake) Soldier: What the hell is that?! (Unit 02 rises from the lake, holding a NERV battleship).
In a more down-to-Earth (sorta) example, we have Misato Katsuragi. She's not only a strong Action Girl, but fiercely devoted to her Children Shinji and Asuka, and especially to Shinji.
Ojamajo Doremi gives us the Ojamajos for Hana during Sharp and beyond. To wit:
Try to kidnap her? They will track you down and use your established weaknesses to lure you into a trap and take her back.
Break out of said trap? They'll use their newfound powers to kick your ass. And they will do this each and every time you try, even when it's the fault of your subordinates.
Run off with her when said subordinates are having a Heel–Face Turn? They will trail you back to your home realm and stop at nothing to get her back.
Threaten her life? They will go against all odds to get the cure even at the cost of their lives.
Instill a hatred of vegetables needed to make her healthy and strong? They will break that curse by any means necessary.
Possess one of the girls so as to bring Hana straight to you so you can kill her directly? The others will follow and do everything to snap their possessed friend out of the spell and will fight tooth and nail to keep you from killing her.
In short, if you mess with Hana and the other Ojamajos find out, be prepared for a world of hurt.
Bellemere, who when given the choice to buy her life or those of her daughters, offered hers in Heroic Sacrifice to ensure Nami and Nojiko weren't killed by Arlong. Even more when you realize that it wasn't until after this proclamation that the bad guys even knew about her daughters who aren't actually her blood. She adopted the girls when Nami was still an infant and Nojiko just barely a toddler, and ultimately decided she would have rather died than pretend she had no daughters in order to spare her own life.
Most recently we have Portgas D. Rouge, the mother of Ace. To escape detection by Marines searching for children being born at that time in an attempt to find the child of Gold Roger, Rouge withheld giving birth and bore her baby in her womb for twenty months out of sheer willpower before finally having him. The act ultimately killed Rouge, but allowed Ace (who would take up her surname instead of his father's to honor her) to grow up in relative safety under the care of Garp and alongside his grandson, Luffy.
In Plastic Memories, Kazuki is this toward Isla. She is very angry at their section chief when he suggests pairing Tsukasa and Isla up together and is quite vocal in her opposition to letting Isla back out into the field so quickly. She also scolds Tsukasa after his first job resulted in complaints filed against them due to Isla destroying a trash can in the first episode.
Mrs. Delia Ketchum of Pokémon would be a more prominent example if Pallet Town was focused on more often. The one time in which her home was threatened, though, she proved to be a formidable force, scaring off Team Rocket and getting a Mr. Mime (her current housekeeping Pokemon) to boot.
Also, there's the pivotal role she had in Pokémon 3: Spell of the Unown. Delia may have not taken physical action, but she was a Guile Heroine who became a key player in helping the emotionally fragile Molly, who had the legendary Pokemon Entei's leash, come back to her senses, which would be vital to controlling the damage made later.
Another example: in the 13th movie, Zoroark is one of these. She apparently has such extreme motherly instincts that she can FEEL Zorua getting kicked around, and promptly gets so pissed off that she (in roughly the following order): punches her way out of a thick metal box that gives her a nasty shock every time she touches the walls (a box that she's been trying and failing to escape for the past half-hour of the movie or so), fights the Legendary Beasts to a standstill on her own, and then utterly trounces Kodai without laying so much as a claw on him.
To make it even more impressive, Zoroark isn't even a Legendary Pokemon and yet she managed all that. On top of that, Kodai can see the future and she outwitted him completely.
One of the DP episodes featured a Froslass that took Meowth and Dawn's Piplup hostage to get Ash, Dawn, and Brock to help her find her missing Snorunt child, who had been kidnapped by a Pokémon poacher.
In the Johto series, a Tyranitar was seen trying to protect her Larvitar child twice, even going as far as attacking Ash and his friends when they showed up to return Larvitar.
The Kangaskhan as a whole. They are very protective of their children and will attack anyone who threatens them.
Tommy's mother was very upset that her husband dropped their child, even though he wore a parachute and was saved by the Kangaskhan.
In Puella Magi Madoka Magica the Movie: Rebellion, Cool Big Sis Mami Tomoe doesn't seem to have Taken A Level In Badass at first... but then Homura kidnaps her friend Bebe (because she thinks Nagisa/Bebe is the witch controlling the labyrinth). Mami somehow saw this coming, had attached a ribbon to Homura so she couldn't escape via Time Stands Still, and proceeds to fight the heavily-armed Time Master to a draw. Wait, no, Mami wins easily, because she did all that with a clone of herself made of ribbons which suddenly engulfs Homura when she finally lands a hit on "Mami".
Sailor Moon: Woe betide anyone who hurts someone Usagi Tsukino/Sailor Moon cares for. Whether it's her boyfriend, her Kid from the Future, her fellow scouts or her muggle friends/family. Especially in the case of manga!Moon, who is quite more ruthless in her defense of her loved ones. One of the most beautiful examples is the end of Super S, where the defeated Nehelenia exacts "revenge" on Moon for her loss by throwing an unconscious Chibi Moon off the edge of the floating battlefield...and after (understandably) BSOD-ing a little, Moon says "You...you won't defeat me," and jumps off the same field to rescue Chibiusa, even transforming into Princess Serenity to save her Kid from the Future. And it ultimately works.
Also Makoto Kino/Sailor Jupiter. Her title of Senshi of Protection isn't just for shits and giggles, you know. When she's feeling dizzy after donating blood in one episode, she immediately goes outside to fight, and when Moon is pinned down by the Monster of the Week, Jupiter goes BATSHIT, forces herself to stand up, keeps attacking and singlehandedly kills the monster.
Minako Aino/Sailor Venus Ami Mizuno/Sailor Mercury have Mama Bear moments in the R season, where they get their first power-ups after facing Cardians who had taken kindergarten children (Minako) and babies (Ami) as hostages.
Moon: W-wow, Mercury! I had not seen that power! How did you get it?
Mercury: I'm not sure. I only know that she made me angry when she threatened the babies!
Senyuu has Cecily in later chapters. Seriously, don't mess with her son Lake or do anything that might endanger him if you want to see the next day.
In Shaman King, the spirit moving the Golem turns out to be Redseb and Seyram Munzer's mother. It is unknown why she only appears to respond to Seyram's commands, and the cause of her death is rumoured to be related to the creation of the Golem, as she is clearly dead by the time the children's father was killed. However, even when her children's bodies have been destroyed and only their spirits remain, she activates the Golem on her own to try to prevent Hao from feeding Seyram's soul to SOF. It is shown that when Hao voices this realisation, Redseb at least was not aware of their mother's presence.
Hao: Impressive. Even in death, a mother fights to protect her children.
Shiki gives us a couple of darker takes on this trope. The more straightforward is Chizuko Murasako, sister-in-law to Masao Murasako, who eagerly takes up the mantle of killing vampires once they learn that they're the ones who killed her son, and who even kills Masao when he comes to her begging for help at the end (having become a vampire sometime previously). Then there's Motoko Maeda, who is driven into deep insanity as her children are picked off one by one, and eventually retaliates by burning down the entire village!Shiki being Shiki, neither one is a truly heroic character, though both are fairly sympathetic as these things go.
In Sora No Woto, mess with any of the girls of the 1121st Helvetian Tank Platoon and you'll get a deadly serious Felicia Heideman.
Marie Mjolnir in Soul Eater is a perky Team Mom to her students. When traitor Justin Law comes to Death City to kill one of them, she frightening and protective figure.
In Toriko we have the female Battle Wolf who has just gave birth to her puppy, Terry. At the same time she ignores the massive, rampaging Devil Serpent who's gorging on the other animals in the arena. However, as soon as the monster look at the cub, she stands up, slowly walks towards him, and then shred his whole body to tiny fragments in one bite.
Lady Chiyo had a Face–Heel Turn and joined the Bishokukai because she wants to use one of the ingredients they are seeking, a legendary rumored ingredient capable of reviving the dead, to bring back the son she lost years ago.
Also, a rare male example, Fai. Don't mess with his Little Kitty or you can go and count your bones. Guess who the Papa Wolf role falls to. Right, Kurogane
In Witchblade Rihoko's biological mother Reina Soho sacrifices her life to protect Rihoko from Maria, a psychotic Neogene. Also, Rihok's adoptive mother Masane Amaha sacrifices her life in order to destroy the Witchblade in order to ensure that Rihoko will not become the Witchblade's next host.
In Yu-Gi-Oh! 5D's, there's Martha, who runs the orphanage in Satellite, whose past charges have included Yusei, Jack, and Crow. Not only is she fiercely protective of her charges (past and present), she's one of the few authority figures whom the three protagonists respect and obey without question; she earned the respect. (Some of this has clearly rubbed off on Crow, who has become a Papa Wolf towards the children of Satellite as an adult.)