Tiger pulls one in Dungeon Keeper Ami. Ami was battleing CrownedDeath telepathicly, during the battle of Crowned Death's High Temple. Battleing and looseing, badly. Tiger possessed Ami while she is possessed by Crowned Death, a move so inherently suicidal that she manages to (metephorically) sneak past the dueling minds and fill the massive, swimming fortress with high explosives useing Ami's link to Crowned Death. She even breifly goes One-Winged Angel doing it, too.
In Chapter 6 of Equal And Opposite Attraction, Hayate is trapped in a pocket dimension of dark magic, slowly being mind-raped into a coma. In the next chapter, Negi hears her cry for help and acts accordingly. However it isn't so much his entrance that's flashy, but rather his EXIT.
With a name like Kyon Big Damn Hero you'd expect Kyon pulls this trope often. You'd be right: saving Tsuruya from a some Yakuzatwice, Kanae from an upperclassman a few days later or to Sasaki when she was being kidnapped he can certainly do the titular trope.
Phoenix gets saved just in time from being attacked by timberwolves while he's lost in the forest by Fluttershy, of all people.
What witness pulls the obligatory Ace Attorney Big Damn Heroes moment by showing up just as Phoenix is about to lose the trial? Surprise, it's Fluttershy again!
Just as Calvin is sentenced to life in Azkaban in The Best Seven Years, Galaxoid and Nebular rescue Calvin by freezing time and teleporting him onto their ship
This happens again in the sequel In Love and War. Calvin breaks into the Predicons base to rescue Susie. They do a pretty good job until they get to the air duct, which eats up a lot of time and ultimately causes them to get caught and captured by Waspinator of all people. And then the Maximals manage to rescue them.
In And Again, Asahina gets one when she jumps in and kicks away Monobear when he tries to murder Chihiro while their strongest classmates are off gathering weapons. This is followed quickly by Mukuro, Sakura and Mondo getting back and opening fire before he can retaliate.
A more recent chapter has not just Sten, but also Alim Surana (the elven mage Warden) and Leliana doing something quite similar, although, in this case, they have to save him from his mind breaking down since the Archdemon's psychic attack is already over.
First, adult Apple Bloom, Lezard, and Spike save Applejack from a group of Neo Canterlotsoldiers that have captured her.
Likewise, Fluttershy saving Rainbow Dash from another group of soldiers about to finish her off after Scootaloo left her for dead.
Shortly after, it looks like Scootaloo's forces are going to finish off the remaining protagonists, only for Rainbow Dash to save Pinkie Pie, causing their Elements of Harmony to evolve to armor, which is followed by destroying the soldiers and sending Scootaloo running.
Applejack breaks Rarity out of the dungeon and as they're escaping they're cornered by the brainwashed Princess Luna, who begins to wipe the floor with them before the other Element bearers burst through a window, and turn the situation into a successful fighting retreat.
In the Pony POV Series, The Final Battle with Fluttershy's Superpowered Evil Side, Princess Gaia/Nightmare Whisper, is going badly. The group are battered, beaten, and bloody, Rarity's pretty much completely out of it with broken legs and no energy left to use magic, and the only way to stop Nightmare Whisper seems to be Rainbow Dash performing a Mercy Kill. Thankfully, Fluttercruel fights her way out of the Jury of the Damned she was being tried by and manifests in the physical world. Not only does she give the others the motivation to summon the Elements, she fills in for Fluttershy as the Element Of Kindness, allowing them to defeat Nightmare Whisper with them.
Part 6 of Shining Armor's Arc has a moment that combines this with Gunship Rescue. When Shining and his griffon allies are about to be killed by General-Admiral Makarov's forces, the rest of Shining's squad shows up, followed shortly thereafter by the rest of the forces under his command, including several attack shuttles. Makarov wisely retreats at that point.
Directly before that, Thunderchild, one of Shining's squad, saved Shining from Makarov, who had him trapped in an Anti-Magic force field spell and was going to beat him to death.
Similarly, in Part 15, a Hooviet army is about to wipe out the village that Misfit Actual and the Anti-Hooviet Rebels are protecting, when Commander Shepherd shows up with every armed ship in Cadence's flotilla and scares them off.
The Battle of Cloudsdale in The Abundance. The abstract Loyalty has brainwashed the masses, Twilight is down for the count and just for fun he decides to drop The Doctor and Dinky to their deaths. Cue two heroic arrivals: first, Derpy Hooves performs a SONIC RAINBOOM to save her daughter and The Doctor... then Trixie arrives with Faith, an army of former prisoners, and a massive airship to turn the tide and win the battle.
Rainbow Dash pulling off the Sonic Rainboom (in this continuity, for the first time since she got her cutie mark) in order to save Esra and Tastar from a giant dragon.
Subverted in The Mixed Up Life Of Brad; when Twilight's boyfriend is being held imprisoned, she arrives and knocks out the guards. Brad imagines that any minute now she'll burst dramatically through the door and deliver a badass one-liner, but it turns out she just wants to talk to him—there's no point in freeing him anyway, as there's nowhere they can escape to. He has to persuade her to burst dramatically through the door (and deliver the one-liner).
A Growing Affection has multiple examples, but most notably: the Jonin backup teams save the Naruto Rescue Squad from the One and Three-Tails. Team Kakashi saves the original Ino-Shika-Cho from the Paths of Pein.
In The Sun Soul, there are more than a few moments when the heroes swoop in to save the day at the last possible second. Although the author seems to like making thempay for their constant heroics.
In Pokémon Mystery Dungeon: Reflecting Balance, the main characters end up walking unprepared into a Monster House in Chapter 14 while looking for the Flygon who can help them find one of the missing crystals that is hidden somewhere in the desert. Luckily, the other two rescue teams that came along to help with the search show up, and distract the wild Pokémon while the main characters look for the exit to the dungeon.
In Chapter 19, the main characters end up in a Monster House again, and while better prepared this time, still find themselves in a difficult spot. Luckily, their friend Azure, who had recently evolved into a Marill, shows up and helps them fight off the wild Pokémon.
Clash of the Elements: Gemini, Geno, and Alpha pull off one of these moments in the very chapters that they end up joining the group in, saving the heroes from the outer guardian of the Lightning Palace, Joe Dark and The Dark Crystal King respectively.
Rosalina does this as well in Chapter 46, saving Mario from dying at the hands of Joe Dark
In return, Mario does this for Alex in Chapter 54 by stopping and destroying Joe Dark's sword from killing him in one-blow
Respawn Of The Dead gives us Scout rushing in whacking the traitorous RED Spy over the head with his bat, when the latter had the Engineer and Sniper at both gun and knifepoint, and had just before been suggesting that he and the Engineer gang-rape Sniper.
The beginning of the "Big Damn Heroes" moment in chapter 20 of Warhammer40000 fanfic ToyHammer starts off with the main character running over a Daemonhost (an Eldritch Abomination that has been summoned from a Negative Space Wedgie to possess an already unlikeable monster) with a battered pickup truck. Then offloading the elite of the Warhammer40000 universe's armies (who have been miniaturized).
Semi-subverted in that he still gets his ass handed to him about five minutes later, giving way to a secondBig Damn Heroes moment in the same chapter by a 10 year old girl (who has the unmodifiable psychic 'fingerprint' of The God Emperor of Mankind.).