In episode 17 of B-Daman Crossfire, Riki and Dracyan defeats Basara in Break Bomber, but Basara and Double Drazerous forcing them to use their special move SIX TIMES in order to win resulted in Dracyan losing his memories.
A variant occurs in Fullmetal Alchemist: Ed deconstructs Pride and reconstitutes him as a helpless human baby. In the epilogue, he's grown up to be a seemingly ordinary child, with no memory of the horrible things he did as a homunculus.
In the 2003 anime version, Al gets his body back at the end and is happy - but has no memory of the events of the series.
At the end of Pokémon: The First Movie, Mewtwo erases all memories of him and the clones he created from the protagonists, to both protect himself from Team Rocket's boss and maintain some semblance of continuity.
Unfortunately the former doesn't take, as seen in Pokémon: Mewtwo Returns. At the end of that movie, he lets the protagonists keep their memories at their request He does get the one he missed the first time around, erasing all memories of the incident except for the fact that he lost.. Later movies don't even try the latter.
Rave Master: Elie saves the whole universe from being destroyed in a massive explosion. Her second case of amnesia was induced by either repressing her memories because she also 'killed' Haru, the boy she loved, in the process or using so much etherion.
Usagi does this in addition to a Reset Button at the end of the first season of Sailor Moon. This was the classic way to end a Magical Girl series; that the show was popular enough to undo this was actually quite subversive at the time. But then, Sailor Moon both made and broke Magical Girl tropes. Oh, and this doesn't happen in the manga, where the girls simply keep their memories.
Tekkaman Blade. After finally beating down the Radam forces (or at least his family-turned evil), D-Boy ends up getting amnesiac for real. In the sequel, though, he got better
He had actually been amnesiac for a while before that - since right about the moment he set off for the Final Battle. He won the entire fight with Omega because the one thing that was left after his memory, personality, and even skills like speech were broken down was Unstoppable Rage.
Happens in Wedding Peach, which isn't surprising given how similar Wedding Peach is to Sailor Moon. The OVA series gives the girls their memories back, too; and, again, the manga doesn't do this.
That's rather misleading and wrong. Technically Wedding Peach for the most part averts this trope since unlike Sailor Moon it was not used in the TV series. It was actually created for the OVA series and then promptly retconned for the girls in the very same episode it was introduced.
Kudou Yoji in Weiß Kreuz Gluhen ends the series with a case of Victory Guided Amnesia following a Disney Death - arguably the best-case scenario, given the character's state throughout the series.
Pharaoh Atem in Yu-Gi-Oh! wiped his own memory and all existence of his very name from history after his initial defeat of Thief King Bakura and Zorc, only to have to scramble to regain both millennia later after both baddies return.
A borderline (And very depressing) case of this combined with A Fate Worse Than Death at the end of Zeta Gundam : After the defeat of Big Bad Paptimus Scirocco, the dying Scirocco, impaled on the nosecone of the Zeta Gundam's Waverider mode, uses his last bit of Newtype power to completely shatter Kamille's mind, making him not only forget everything that's happened up until then, but basically putting him in a greatly diminished state of mind that is somewhere between vegetable and a young child. He gets better by the end of ZZ Gundam, though. And not before he spends several episodes of ZZ's second half as a Rare Male Example of The Ophelia, either.
A Certain Magical Index has a subverted example at the end of the series' very first arc. When Index goes Brainwashed and Crazy on her friends, she casts the spell "Dragon Breath" that causes feathers to fall from the sky. Coming into physical contact with just a single one is instantly fatal. When Touma undoes her brainwashing with his Imagine Breaker, he gets distracted by relief and one of the feathers graze his head. He survives due to Plot Armor but as a result of brain damage, all of his memories are destroyed permanently. He's fully aware of what happened but he can't undo it so he keeps it a secret and pretends nothing's wrong to keep his True Companions from worrying. He's so good at it in fact that neither of his primaryLove Interests figure it out until very late into the novels.
Another features this as a natural side effect of successfully breaking class 3's curse. The cause of the curse is the presence of a student who is, in fact, Dead All Along. The protagonists learn that if you find and kill that student, the curse goes away for that year. However, because memories are implanted to hide the "Extra", those false memories go away instantly. How fast depends on how aware you were of what had happened. As the first one to do it and our protagonists are able to leave behind a message for future students of class 3 to try and make them aware.
The 3rd movie of Puella Magi Madoka Magica (Puella Magi Madoka Magica The Movie: Rebellion) has this in an ominous sense; in fact it might even be an inversion depending on the viewers perspective. Homura takes over the God position of Madoka and creates a new world where both Madoka, Sayaka, and possibly other former witches are still alive. The new world, essentially, is one that every magical girl says they want. Sayaka and Madoka's memories are bound too; with Sayaka slowly getting Wistful Amnesia. However, Madoka's eyes still flicker gold indicating her power is still there. The whole thing is a Sequel Hook.
In a Retcon to explain the amnesia of Namor the Sub-Mariner in his first post-Golden Age reappearance, it was later said that in his final battle with the powerful psychic Destine, Namor was hypnotically commanded to fly as far as his little wings could take him, and simultaneously to forget his own identity. He wound up spending nearly a decade (or several, after the Sliding Timescale got through with him) as an amnesiac derelict in the Bowery with a fear of water.
Marvel Comics' The Sentry - the world's greatest hero - saved the world from The Void, then makes everyone forget they ever heard of or met him, and he forgets he's a superhero. It takes The Void returning for him to remember, and slowly others do too. Note that is entirely Retcon... The Sentry was created with this Back Story already in place.
It eventually turns out that it is actually backwards - his regaining his memory it what causes The Void to return, as it is his Enemy Without, and the whole amnesia thing was a Memory Gambit to keep The Void from being able to manifest.
Occurs when Zach and Jenny return from the Door At the Edge of the Universe in the first volume of Scott McCloud's Zot!
Tintin and his friends didn't so much save the day in Flight 714 as save themselves from the bad guys, but either way their memories (as well as those of the bad guys) are wiped by aliens at the end of the story, leaving only Snowy in the know.
In the backstory of the movie Hook, Peter Pan got this after he left Neverland. Much of the plot hinges on him (now grown up) needing to relearn his basic heroic abilities (fighting and flying) in order to defeat a vengeful Captain Hook.
After the protagonists finish playing Jumanji, time is reset back to 1969, before Alan and Sarah started playing the game. They remember the whole thing but Judy and Peter apparently don't remember, presumably because time was reset to before they were born.
Used once or twice in the original Oz books by L. Frank Baum, where the heroes tricked the villains into drinking from a fountain containing the Water of Oblivion — an amnesiac formula so powerful, it left the drinker still able to walk and talk...but not much else.
The ending to Sphere is open to interpretation. I always thought the one chick that seems to be more in control of her manifestations decided to keep her power and use it to make the others forget. But it's hard to tell exactly what's going on because of the fact that the narrator gets/claims amnesia.
At the end of Susan Cooper's The Dark Is Rising series, the Lady chooses that John Rowlands forget everything that happened so he will not have to remember that his wife Blodwen was the evil White Rider. Merriman wipes the memories of the Drews and of Bran Davies.
In Will Eliot's The Pilo Family Circus, ex-clown protagonist Jamie uses some of his wishing powder to erase his memories of the circus. It doesn't work too well, as the Eldritch Abominations imprisoned below the circus - along with Jamie's boss, Gonko- keep trying to remind him of his experiences. And since he still has half a bag of wishing powder left, it's implied that he will one day use it to restore his lost memories, with catastrophic results.
It is more likely that Susan was allowed to survive the crash so that she had a chance at believing in Narnia again
In at least two of Andre Norton's novels (Android at Arms and The Crystal Gryphon) one protagonist wins the day by calling forth a powerful force that acts through them - but since they weren't in control at the time, they can't remember exactly what they did, or how. The latter had a sequel, in which the hero eventually learned to use power himself, without losing his own identity in the process.
In the fourth book of the Sword of Truth series, Temple of the Winds, Richard is only allowed to leave the temple by losing all the knowledge he gained from entering (which is to say, quite literally, everything there is to know about being a War Wizard; it's perhaps the only part of the series where he is in full control of his abilities). Perhaps an odd example, as he does remember the events that happened.
In Stephen King's IT, the children (except for Mike Hanlon) begin to forget almost as soon as they beat IT and most of the as-adults portion of the novel is spent with them trying to remember. Once they beat IT the second time, their memories fade again (including Mike's) within weeks.
At the end of Brave Story, Wataru can still remember his journey... but it's stated that he will forget slowly, instead of all at once. This is especially sad, as he used his wish to keep all of his friends in Vision safe.
In The Eternity Code, Artemis Fowl comes up with a scheme that will let him reclaim the stolen C Cube, but he requires fairy technology and the only thing he can offer in exchange is his own memories of them (which they long wanted to erase to maintain The Masquerade). Of course, being the Magnificent Bastard he is, Artemis finds a workaround...
In The Hounds of the Morrigan, the Dagda erases the memories of the two Kid Heroes—presumably because they saw an absolutely horrifyingGorn-tastic battle. However, he favors them always afterwards, and gives them back gifts from their journey—such as the Hidden Valley's daisy-patterned china, their ship kite, and, best of all, their friend Cooroo the fox.
In Passage to Dawn, the 10th book of The Legend of Drizzt, Harkle Harpell uses a spell called "The Fog of Fate" to help the heroes solve a riddle. He ends up giving them too many hints, straining the limits of the spell, and as a result, is catapulted back home, having lost all memory of his participation in the quest.
In Devon Monk's Allie Beckstrom novel Magic to the Bone, Allie throws around a lot of magic at the climax. It has already been established that using magic can cause holes in her memory.
The last book of Stephen King's "Dark Tower" series ends with Roland finally reaching the Tower after years of questing, only for it to show him a sort of presentation outlining his many failings as a person, then sending his soul back in time to the start of the first book. He has just enough time to be horrified before his memory is reset. A pretty poor way to treat a man who has literally saved countless realities from destruction. King himself didn't like the ending, and included a page telling the reader "stop now".
Live Action TV
Both the classic and the new series of Doctor Who have used this trope.
In the fourth season finale of the Doctor Who revival, companion Donna Noble gains the Doctor's memories and brain power and uses it to defeat the Daleks. Afterwards, the Doctor reveals that the mind of a Time Lord is too much for a human brain to handle and, to save Donna's life, he wipes her memory of everything she experienced since meeting him. He warns her family that if she ever finds out about her adventures her mind will destroy itself.
The classic series used this in "The Invasion of Time", where an aftereffect of the super weapon he'd just built erased his memory of said weapon, as well as The Plan he'd just executed (and screwed up).
And at the end of "The War Games" too; after calling down the Deus ex Machina - the Time Lords - companions Jamie and Zoe have their memories of all their adventures (bar the first) with the Doctor wiped and are sent back home.
"The Day of the Doctor" has this for the past versions of himself the Eleventh Doctor interacted with. Due to their meeting throwing their Timeline out of sync, the past Doctors will not clearly remember what happened once they came together. Until the Doctor reaches that point via The Slow Path, he'll never know that he was able to save Gallifrey instead of being forced to destroy it.
Happened to Daniel Jackson in Stargate SG-1 both times he returned from Ascending to a Higher Plane of Existence. But not completely; he was left with a certain degree of knowledge he had gained whilst ascended, and the potential to remember more of it (later becoming a major plot point).
The Star Trek: The Next Generation episode "Clues" deals with the crew realising they've lost an entire day, though they didn't really win or lose the "battle" fought during that day - they just reached a stalemate for which one of the requirements was a mind wipe. The first attempt failed because Data was immune; the second time, the crew agreed to it (and Data agreed to help cover it up), but they missed some details. The third time, they fixed those details and it finally worked.
Set up ahead of time in one episode of Dollhouse. Echo and several other Actives are given their original functional memories (without any declarative ones) and allowed to do as they please so that they can fulfill the desires that are causing trouble in brainwiping them later. As soon as they finish whatever it is they set out to do, they black out, leaving them ready to be put back in the chair.
On Twice in a Lifetime recently deceased people would be granted a chance to go back in time and convince their past self to make better choices in life. Once they succeeded they were returned to the present where in the new timeline they were still alive and leading a good life. They would briefly remember both timelines but then the memories of their time travel adventure would disappear and they would only remember the new version of events.
As quoted above, the Tenacious D song "Tribute" is a tribute to the "greatest song in the world" that Jack and K.G. performed to defend themselves from the Devil. However, after this event, the actual song fades from memory, but they know it wasn't anything like "Tribute" itself.
In Promethean: The Created, when a Promethean reaches the New Dawn, they make a roll that basically determines whether they've been acting more human than Promethean (bonuses for fulfilling Vice or Virtue, penalties for using Transmutations). If they succeed, they've been leaning towards human and remember everything; if they fail, however, they've been leaning towards Promethean, and everything pertaining to the Pilgrimage is boiled away. Leaving them with a strong case of amnesia and likely no record of existence... but the universe no longer hates them.
In Pokémon Live!, Mewtwo wipes Ash's memories of his appearance and the fight with Giovanni; it may have been accidental given he hit MechaMew2 with enough of Ash's memories to make him faint.
BIONICLE: After successfully summoning the Toa in Quest for the Toa, Takua is thrown across the island and forgets everything. However it's not permanent, and Takua regains his memory in the first Mata Nui Online Game, which picks up immediately after Quest for the Toa.
Except they do if you're playing the GBA release; according to the scrolling text at the end, they're the ONLY ones that remember what happened.
The NES version, on the other hand, makes it clear that the only person that will remember their victory is the player.
In Metal Gear Solid Mobile, Philanthropy's first mission is revealed to be a VR simulation, with a kidnapped Snake locked into the sim and taking orders from an artificial Otacon, while the real Otacon was on the sidelines, attempting to hack Snake's brain out. Eventually, he was forced to complete the simulation to get out, but, as he failed to provide the data his captors needed, his mind was wiped of the event and he was returned to Otacon. Gets especially glaring when you realise Otacon would still remember. Gets even more glaring when you realise it wouldn't even cause a real continuity problem if Snake remembered the events and would even help justify his seemingly irrational distate for VR in Metal Gear Solid 2.
The bad ending of Shadow Hearts 2 has Yuri lose his memories and identity as a result of a curse literally wiping his soul clean. In the good ending, he commits suicide before that can happen. This lets him retain his personality (if not his memories) and his love for Alice, which lets him travel back in time to be by her side again.
After saving the world in Soul Blazer, the Blazer (who was created by God to save the world) has returned to heaven as his work is done. A year later he misses life as a human and the girl he had met early along the way. So God turns him back into a human at his request, but with the cost of losing his memories. He pops back into existence next to the girl in a field, who remembers him and starts their relationship anew.
You pass one of these in Baldur's Gate 2. In the Spellhold asylum, one of the inmates is a former bard of repute who, in his search for the answers of the universe, is mentioned to have gotten too close to something that didn't like him poking around. You have no way of knowing what really happened, but his mental faculties are now at the level of maybe a 5-year-old, he talks about little except his "many many pretties, piled high beyond the skies" and has an infinite and inexplicable supply of precious gems.
At the beginning of Chain of Memories, Sora loses all recollection of the events of the first game. At the end, he gets them back, but only if he gives up his memory of this game in return.
Done twice in 358/2 Days, where beating the second-to-last boss costs Roxas all his memories of his best friend in the world. Beating the final boss costs him every other memory.
Also at the end of Birth by Sleep, where Terra's ultimate triumph ends with him possessed by the villain and both of them mind-wiped.
And in the secret movie "Blank Points," where it's revealed that Ansem the Wise survived going down with his ship at the end of Kingdom Hearts II, but the end results gave him near-total amnesia.
And once more in Coded, where Data Sora finally succeeds in rebooting the jounal's data...but since he's technically part of that data, he's rebooted, too. When we see him one last time, he doesn't remember a single thing anymore.
Both the supposed Big Bad and supposed Big Good of Arcanum, due to voluntary or involuntary isolation, are shadows of their legendary power.
Implied in Final Fantasy VII, albeit in a very screwy way: Zack manages to achieve victory (protecting Cloud from Shinra), but Cloud is the one who ends up with amnesia.
This is a source of trouble at the ending of Devil Survivor 2. It is possible to restore the deleted world through the power of the Akashic Records, but the problem is, you need to prove yourself stronger than your past, leading to a series of battles with shadowy monsters created from each characters' past files.
Gage has his memories wiped in The Journeyman Project 2 at the end of the game after proving his future self's innocence. This prevents him from accidentally causing a paradox by changing his behavior when the events leading to his arrest take place.
In 3 future Gage reviews the video of his exploits in 2 and wishes he had been allowed to remember Arthur.
Futurama, "The Why of Fry": Nibbler wipes Fry's memories after he saves the universe from the brainspawn.
This is repeated several more times to the point of parody; Bender's Game shows the characters unfazed by Nibbler's speech because he forgot to erase their memories last time.
Also, everyone on Earth (except Fry) forgot about the Brainspawn after Fry foils their invasion.
At the end of It's Your First Kiss, Charlie Brown, Charlie Brown doesn't remember that he worked up the nerve to kiss the Little Red-Haired Girl at the Homecoming dance and subsequently was the life of the party.
At the end of the Kim Possible movie "A Sitch In Time", none of the characters remember saving the future from being taken over by Shego thanks to Ron breaking the time traveling monkey that caused the whole mess to begin with.
Transformers Prime, after Optimus Prime stops Unicron from reviving with the Matrix of Leadership, he loses his memories of the Autobot-Decepticon war. And thinks he is still Orion Pax as well as friends with Megatron.
Codename: Kids Next Door: Monty Uno (a.k.a. Numbuh Zero) defeated the villain of The Movie by using a device created to erase the memories of decomissioned KND operatives.
Double-sided subversion: he and his wife get better BECAUSE his son is getting a promotional transfer to another planet, with little chance of coming back.