Sekiseki, a mineral which blocks reishi, is why Soul Society cannot be invaded; it blocks any and all forms of spiritual power. This doesn't stop the Vandenreich from marching right in, three times, and curbing the Seireitei because they are quincy. They absorb reishi and all of Society is made of reishi.
Rukia's gigai makes its wearer invisible to sensors by nullifying reishi
Sakura Sakurakouji with implied Anti-Magic abilities. All Code Breakers' abilities have been shown to be ineffective against her, and she's displayed the ability to cancel out the effects of those powers on others. Canceling out their power's effects may or may not require full body contact, since she seems to hug people every time she does it, causing her friends to name it her "rare power hug attack."
The President is also a power-suppressing "Rare Kind" and Sakura's biological father.
The President made Inoichi with this ability in mind, although she has to bite someone to take their power rather than just touch them.
In Code Geass R2, Jeremiah Gottwald obtains a Geass Nullifier ability along with his second, more complete, more badasscyborgization. It works similar to Anti-Magic in that it creates a field where Geass abilities (and their otherwise premanent effects) are dispelled. He can activate it at will to negate nearby Geass effects, and also triggers automatically whenever Jeremiah himself is targeted by a Geass.
Nana of Elfen Lied can use her vectors to temporarily disable other Diclonius's vectors.
Father of Fullmetal Alchemist can negate the powers of Amestrian alchemists by stomping his foot. He does this by creating a cushion made of souls that reside in Amestris. Xingese alchemy works differently so he can't stop it, or stop the kind used by Scar (which is a hybrid of the Amestrian and Xingese systems developed by Scar's brother).
Main character Mikan Sakura from Gakuen Alice has, as one of her Alices (special powers), the ability to nullify any other person's Alice.
Miroku has one in the form of his arm beads which contain the Vortex in his hand. Since the Vortex is sometimes useful, he simply removes the beads.
Houriki in general, which has the ability to purify and/or seal things, especially Youki. The biggest example of this is Mt. Hakurei, which would instantly purify any youkai that gets too close to it except Kanna, who, as she represents nothingness, has no youki of her own. Inu Yasha was instantly turned into a human once he got too close, while Sesshoumaru was able to temporarily resist the purification due to his sheer power but ultimately had to leave.
Giorno Giovanna of Manga/JoJo's Bizarre Adventure gains this when he gets his new stand Gold Experience Requiem, not only does it nullify any power used on him, but any action taken that could harm him directly or indirectly.
Asuna from Mahou Sensei Negima! has the ability to completely negate magic. This can be very useful in combat, or very bad when it gets out of control. Especially when she's in a flying city that's being held aloft with magic.
In Naruto, Neji Hyuuga demonstrated his skill in closing off the chakra pathways of his opponent (and cousin) Hinata. While this does not initially injure her, it prevents her from using her own ninja powers as the fight progresses. She was aiming to do the same thing to him, as they use the same fighting style, but Neji was more experienced and skilled at it and was even able to reverse Hinata's attacks so that she gets chakra points sealed even when he was the one getting hit. In his next fight Neji does the same thing to Naruto, but he's unaware that Naruto is the host of the Nine-Tailed Fox and thus has two chakra networks instead of the usual one.
Salt water paralyzes devil-fruit users but it doesn't necessarily negate their powers. This becomes important when Luffy is stuck underwater; his neck can still stretch.
Seastone possess similar properties and so it is used to make handcuffs and jail cells for devil-fruit users. Inside them they are no different than normal humans.
Blackbeard has the ability to nullify Devil Fruit users' powers on touch which came with the power of the darkness-based Yami-Yami Fruit.
In Rurouni Kenshin, the Forest of Darkness negates a warrior's ability to sense chi.
Suzumiya Haruhi: Yuki Nagato is able to do this due to the fact that she understands things on a data-level and has the abilities to work on it, it isn't hard for her to nullify any kind of Eye BeamHaruhi makes Mikuru have, by using the right countermeasures. That includes conventional laser beams, hyper-vibration particles and even micro black holes.
Lina at one point gets a magic-nullifying circlet stuck on her head. Only, as she points out, it's not that it nullifies magic; it's that it causes horrible feedback when she tries to use her powers, so basically all she's doing is shocking herself. Once she decides to ignore the pain, she manages to cast a spell and shock her captors by grabbing them right before she sets off the shock.
Later played more seriously when she's the victim of a curse that robs her of all of her magical powers, so she has to go searching for a cure alongside Xellos. In the end, she had to kill the demon Mazenda, since her death was the only solution.
A Certain Scientific Railgun gives us "Capacity Down": it's a sound that, when played over loudspeakers, causes intense disorientation to espers as well as making them incapable of using their powers. The Big Bad puts it to use by supplying it to a gang that's comprised solely of Level 0's (and thus would be unaffected by Capacity Down), and then later using it on the good guys in the finale. It backfired on her in the latter case because she was unaware that the good guys had a Level 0 among them, who was able to subsequently destroy the computers playing the audio.
A "Capacity Down" device later shows up on A Certain Magical Index. Accelerator counters by throwing a car at the enemy base from a safe distance.
Gundam 00 has the Trial System built into the Nadleeh/Seraphim. When it's switched on, every mobile suit connected to Veda shuts down while it's active. It doesn't sound so bad but when you realize that in season 2, Veda was controlled by the Big Bad who used it with every single mobile suit he and his underlings built, it could easily become a Story Breaker Power. On the other hand, said bad guy's control of Veda meant that he could forcibly disengage the Trial System remotely. So naturally, it's almost never used except in the series finale where it simultaneously puts every single mook out of commission as soon as the Big Bad no longer has access to Veda.
In Sekirei, Seo has the ability to nullify a Sekirei's powers if they get within a certain range of him. It was given to him by his best friend Takehito, and he's put it to good use from time to time.
The eponymous organization Pandora from Pandora Hearts utilizes Power Nullifiers in the form of seals engraved on the dungeon floors in order to restrain contractors and keep them from summoning their chains. After the Baskervilles take over Pandora, Oz is taken as a prisoner and confined in this way.
Andy Hinomiya's esper power in The Unlimited Hyoubu Kyousuke. His ability makes him an outcast among both muggles and espers. It also makes him a fairly effective double agent, since he is immune to psychometry and mind reading.
Characters in Hunter × Hunter are able to learn nen abilities that disable other people's nen. The two shown so far are Kurapika's Chain Jail (which will kill the user if it's used on anyone other than the Phantom Troupe) and Knuckle's Hakoware (a bank loan-themed ability that actually makes the target more powerful with each hit, but accrues interest every ten seconds, shutting off the target's nen for a month if they go over a certain limit and "bankrupt.")
Kurapika was able to use a different technique to the same effect, implanting a nen spike inside a person's heart under the condition that it will kill that person if he ever uses nen again.
In Shakugan no Shana, when Shana is captured in season 3, she has a small chain wrapped around her wrist that stops her from using her powers.
In the The Twelve Kingdoms anime, Enki is subjected to a very nasty version of this. Not only he gets one forcibly put on him, but a similar one is placed on a lady who works for him and Shoryuu - if one of them tries to remove the nullifier, the other will be hit by the magical backlash and die. In the end, the lady decides to sever Enki's cord while clearly knowing it'll kill her, allowing him to escape and rejoin Shoryuu.
In the 90s The Flash series, Savitar was able to take all the power of the Speed Force for himself and his minions, with only Wally being able to resist the drain.
Powers, a comic series about human detectives investigating crimes involving the superpowered, has devices called "drainers" that prevent superhumans using their powers while being questioned or detained.
Gold Kryptonite could permanently remove the powers of Superman and other Kryptonians, and exposure to a red sun would do it temporarily, as would some varieties of Red Kryptonite. It was brought back after 20+ years but its effects are only temporary. This makes it less scary but more useful as a plot device: depowering Supes forever isn't an option, but you'd be surprised how long fifteen seconds is when you're depowered and a superpowered nutjob is trying to kill you to death.
The X-Men put something like this on Magik to keep her from escaping when she was made part of the "Extinction Team". (The conditions didn't come with a pardon, and she was only allowed to leave the X-Brig for missions; her suit had a lethal failsafe to prevent her from escaping via teleportation; maybe the problem was simply that it was too dangerous for casual use.)
Another mutant, Leech, had this ability as his own mutant power, and on occasion, it's been shown to work on non-mutants. He later showed up in the third X-Men movie, where he was the source of the "mutant cure."
Another time, Storm was robbed of her powers temporarily by a device created by mutant inventor Forge.
The Mutant Cure was developed by Dr. Kavita Rao and made available to mutants everywhere in Astonishing X-Men. As in the movie, they're so offended by it being called a "cure" that Wolverine violently attacks Beast to prevent him from taking it, out of fear he would become the poster child for mutants Blessed with Suck wanting to do something about their condition.
The Marvel Universe contains the Ultimate Nullifier, which... nullifies anyone's power, including heavyweights like Mephisto and Galactus. There's a rookie underground hero calling himself the Ultimate Nullifier, with pistols modeled after the famous weapon that temporarily depower anyone they hit.
Moreover, the Initiative made use of SPIN technology to keep its recruits in line — and enforce the SHRA. SPIN removes any and all superhuman abilities permanently. After Komodo was dosed when she refused to go along with the corrupt Initiative of Dark Reign, they managed to develop a "cure" of sorts to restore her powers.
In another Marvel comic called DP 7, there is a character whose power is to cure paranormals of their powers. In this story, however, there is a cult of paranormals who believe that their powers are a gift from God, and that to remove those powers is blasphemy.
Harold Nelson, aka "The Rainmaker," from PS238, is able to do this, as well as enhance meta-powers. Suppressor devices, in the form of temporary ray weapons or permanently attached devices also appear.
Scrambler, a member of the Marauders super villain team in the X-Men comics, has the ability to disrupt and suppress the powers of other mutants. When he comes into contact with Rogue, their powers interact in such a fashion as to temporarily strip both of them of their superpowers. Same thing happened when the comic version of the aforementioned Leech grabbed Rogue's face. The rest of the Morlocks immediately found out that someone who hangs around guys like Wolverine don't need any powers to kick the ass of anyone who doesn't seem to have any powers beyond "looking like an extra from a Mad Max film".
The fourth Empowered collection introduced a villain with this power named "Wet Blanket." Not only did he nullify powers, he also nullified his fellow villains' enthusiasm with his attitude.
The DC Elseworlds story The Golden Age provides the 40's superheroes a Deus Exit Machina from World War II with the power-nullifying Nazi Parsifal. After several heroes were nearly killed by Parsifal, FDR ordered them to all stay out so that a superhero's death didn't hurt morale.
Another DC Elseworlds story JLA: Act of God had a giant cosmic storm wash over earth and permanently negated everybody's powers leaving only Badass Normal and tech-based heroes/villains to fight/commit crime (even some of the more fanciful super tech, like Green Lantern's ring, stopped working.)
In Ex Machina Mitchell Hundred, formerly known as The Great Machine, gave his two civilian assistants, Kremlin and Bradbury, each a device capable of nullifying his abilities. As a lifelong fan of comic books he was well aware of the danger that he could present if he ever decided to stop working for the public good, and he was also aware that many people are never accepting of the fact that they have changed and are no longer the "good guy." As such, he wanted these two men, who he alone trusted with the secret of his powers and identity, to have the capability of shutting him down if they ever thought that he could no longer be trusted. In the last arc of the series Suzanne, who has become possessed by the power and is working to destroy the world, steals Kremlin's nullifier and goes looking for Mayor Hundred... only for Mitchell to reveal that not only did the nullifier not work, but it had never worked. He knew that Bradbury and Kremlin had been nervous even if they never said so, so he gave them each a piece of junk filled with electronics in order to reassure them of his good intentions.
The Savage Dragon villain Negate has the ability to permanently remove the powers of anyone who acquired them through "unnatural means"(i.e. anyone who isn't an alien, supernatural entity, or born with powers). He's eventually used by the Evil Overlord Darklord as the key component in a "nega-bomb" that depowers the entire world.
In All Fall Down, Sophie is a walking one, and IQ Squared designed a device to do this to super-powered villains in prison... including his father.
In the New 52, Rose Wilson emits a field that turns off invulnerability in her presence, which allows her to fight people like Superboy.
In Uncanny Avengers, the S-Man Goat-Faced Girl can shut off the powers of mutants simply by looking at them.
A common thread in My Little Pony: Friendship Is Magic fan fiction is the need for these sort of devices, typically a ring or other covering placed on a unicorn's horn as a law enforcement restraint on unicorn magic (although one ends up in Wild Sweet And Cool as sports equipment). Effectiveness varies; one fic might have a simple ring work on any pony, even Physical God Luna, while another might have various grades (including one which MELTS when Twilight Sparkle is pissed off sufficiently).
The Kamen Rider Double film Double Forever A-Z/The Gaia Memories of Fate had a new evil Rider named Eternal. Eternal's Maximum Drive Finishing Move initially was capable of permanently disabling any old-generation Gaia Memory, regardless of whether they were a Rider's or a Dopant's.
The titular high school in Sky High has such a device in its detention room.
Superman II allowed Superman to become "permanently" human by absorbing an extremely large dose of red solar radiation. When the Phantom Zone villains arrive on Earth, however, he regains his powers by consuming the energy stored within the Fortress of Solitude. (This is only revealed in the director's cut; the original version has a Deus ex Machina transition between Superman staring at a crystal and reappearing fully powered).
When Logan first arrives in the past, Charles doesn't have his psychic powers to verify his story or make their mission easier. This is because he's been taking a serum that lets him walk, at the expense of suppressing his telepathy. Considering the Heroic BSOD he's in the middle of, he doesn't mind. The same serum lets Beast look normal with no apparent ill effects, but it has to be taken periodically by both of them.
Nullification collars are used in the Bad Future on mutants in the Sentinel-controlled camps.
In The Dark Hunters series, the magical ability of Were Hunters to shapeshift can be stopped by metriazo collars. If they stay on, however, the Were Hunter will eventually explode from the pent-up magick.
The Trump Card virus, developed by Dr. Tachyon, is meant to cure Xenovirus Takis-A (colloquially known as the setting's eponymous Wild Card). Unfortunately, it is only about 5% effective, and itself lethal in about 30% of attempts. Not surprisingly, most of those who tried it were jokers rather than aces, and even few of those would risk it. And a successful cure can also spell the death of the former wildcarder if his powers kept him alive.
Mai Minh, the Vietnamese Ace healer, can permanently reset wildcarders back to nats. While no Aces were known to ask for healing, she would possibly reset powered jokers and joker-aces.
Croyd's personal strain of the Wild Card during his Typhoid Croyd period is this trope mixed with mass empowerment, being a forced reroll in the setting's Super Power Lottery. It can turn anyone to any wildcarder - nat, joker, deuce or ace to carrier, Black Queen, joker, deuce or ace. From ace to joker, deuce or Black Queen is this trope in permanent or lethal form.
The Astronomer lists the ability to suppress a psychic ace (and thus almost anyone) among his powers. When opposed by Cordelia Chaisson and Demise, he finds out that suppressing only one of them at a time isn't enough...
In Kurt Vonnegut's short story "Harrison Bergeron", people with above-average intelligence (i.e. those who can retain a coherent train of thought for more than 10 seconds) must, by federal law, wear headphones that, every 10 seconds, transmit an extremely loud noise to shatter their train of thought. Also, above-average beauty must wear ugly masks, above-average strength must wear weights, etc. The story shows the logical conclusion of "everyone must be equal."
The Perry Rhodan universe has a variety of devices that counter or dampen psionic powers either on purpose or as a side effect of their normal operation, from actual traps and prisons that negate such powers inside a given area to relatively common force fields that they cannot penetrate (usually a painful experience for teleporters in particular). Justified in this setting by these powers and much of its advanced technology both invoking fundamentally the same hyperspace physics and energies, which can then naturally end up interfering with each other as the plot demands.
In the Black Company books, there's the White Rose, a very mighty Power Nullifier in human form. (There are no superheroes in the books, but magic exists.)
In the Star WarsExpanded Universe, The Thrawn Trilogy introduced the ysalamiri, a non-sapient species of furry reptiles, with the unique ability to suppress the Force in their personal areas. This ability evolved naturally in conjunction with a local predator species, vornskrs, who evolved with the ability to use the Force for hunting. Thrawn is the first to (re)discover their ability, and puts them to various uses. He keeps one on his person, to protect him from Force attacks. He also uses them to speed-grow clones, since the presence of the Force will warp a mind that ages twenty years in a few weeks.
Combined with Capture the Flag in Star Wars: Jedi Outcast: one of the multiplayer modes is called "Capture the Ysalimari"; you can't use the Force while holding it, but nobody can use it on you either.
Used in Sword of Truth when Violet and Six strip Richard of his magic.
In The Wheel of Time series, it's separating a channeler from the True Source. It's called "gentling" when done to a man, "stilling" when it's done to a woman; the gender-neutral term is "severing". It is possible to reverse the process, but it only works completely if the person restoring the connection is of the opposite sex of the person who was severed, otherwise their channeling strength will return at a greatly reduced capacity. More temporary 'shielding' is possible to cut channelers off, and certain places such as stedding and the city of Far Madding are permanently shielded.
Grey Murphy of the Xanth series has the power to nullify magic in any target he chooses, or increase a subject's magical talents or properties through a "rebound" effect.
The prize-winning series Way Home by Vladimir Zykov features both magical slaves' collars and the combinations of those with this trope, using Anti-Magic, known as "black collars". One of the protagonists survives being put into one, manages to break it and learns to break them on others.
Philip K. Dick's classic novel Ubik is about employees of an entire agency of Power Nullifiers. They are a necessary service, since telepaths and other people with potentially dangerous Psychic Powers are commonplace in the setting.
In Shadow Ops, anyone who can use magic can Suppress another magic-user's power. This is integral to controlling magic users, and Suppressing someone in the middle of, say, flying, can have nasty consequences. While other branches of the US military actively use their magic offensively in the setting, the US Marine Corps uses "Suppression Lances" that consist of squads of magic-users whose sole job is to Suppress enemy magic-users and kill them with conventional weapons.
Temples dedicated to Galla, the resident Physical God of Anti-Magic, permanently suppress all magic within. Galla himself controls this effect and magic within his temple and can switch it off as he likes.
Mages abdicating from their Great House and joining Galla's Heresy also forfeit their and their children's magic in favor of a single effect, Galla's Sacrificial Tentacle.
Inquisitors, a rare breed of human mages, can use faith from human crowds to temporarily remove all magic from a wide area. The few genuine witch hunts happened when a priest unknowingly possessed this power. The effect also causes suffering and pain to Witch Species members. Said Witch Species members have long since found out that fully mundane hired guns work just fine if you suspect a possible Inqusitor; the Churches who are in on The Masquerade safeguard potential Inqusitors as a system of checks and balances.
In Miloslav Knyazev's Full Set series:
Splinters from a freshly shattered altar stone nullify both offensive spells cast by priests of the offended deity at the splinter's owner and the priests' defensive spells when attacked by the owner in any fashion (melee, ranged, magic).
Tools used to shatter said altar stone become extremely effective weapons when wielded against priests of the thus offended deity, and will inflict more damage on all priests of all religions in general. A splinter used in this way can be shattered again with the same tools to produce more splinters, but the altar debris will quickly become common stone.
Fruit from the elven divine Trees of Life (which the protagonist nicknames elven acorns and oaks respectively) has the same effect on elven priests of the respective Tree.
Sites which suffered a rare and specific kind of magical damage during one of the Great Mages' Wars will now render mages powerless.
An archmage uses a power nullifier device of possible pre-war origin to temporarily shut down an opposing sorceress' external power source and is cut down by her muggle husband with a mythril sword.
A dragon female uses an anti-dragon amulet of unknown origin during a duel with an unwelcome male dragon suitor. Both male and female are forcibly reduced to their humanoid form, which allows her human and elven allies to kill the male. Later research shows the amulet inscription to say "temporary" without a frame of reference, which may mean centuries for dragons.
In V. Ivashchenko's novels across all settings various sides in various conflicts will use both stationary and mobile means to capture and detain mages. The Black Earl series describe a holding cell in an elven castle and forged restraints (collar, handcuffs, manacles) used by human law enforcers.
A variation in Sergey Lukyanenko's Last Watch is an artifact called the Schrödinger's Cat, which takes the form of a furry collar with teeth. Any use of magic causes the Cat to kill the wearer. Only the Other who places the Cat on the neck can take it off. It doesn't prevent magic from being used on the wearer.
Forever Gate: The gols use bronze collars to prevent humans from using their innate Shock and Awe powers. They are refered to as "bronze bitches" by said humans.
The Quest of the Unaligned: The city of Tonzimmiel is surrounded by a force field which strips the magic from anyone who passes through it. Originally built to make the city a safe haven from the Magocracy that rule the surrounding country of Caederan, 600+ years of the field's effects have caused Tonzimmelians to cease believing in magic altogether.
A Mage's Power: There are runes which are known as "prison runes" because they are used to prevent criminal mages from using their powers to escape.
Tahart hides them in Annala's maid uniform to make unable to resist him.
When Eric is arrested, a metal collar is snapped on him to prevent him from attacking the officers.
Live Action TV
In Mutant X, tags (called Subdermal Governors) bolted into the back of the neck were used to nullify mutant powers, though it seems more to torture them when they try to use them than to truly nullify the powers.
Buffy the Vampire Slayer's 18th birthday present was to temporarily lose her powers and then be forced to fight a vampire, in a test called the cruciamentum. While she was hypnotized, her Watcher was forced to inject drugs into her that suppressed her strength.
In Heroes, the mysterious Haitian has, in addition to memory erasing, the power to suppress other people's powers around him.
The Shanti virus and some pills used occasionally by the Company suppressed powers. It should be noted that the Shanti virus eventually killed the infected.
The characters captured by Nathan Petrelli's goons have a device taped to them that sprays some sort of drug into their nose. It weakened them enough to the point they couldn't focus enough to use their power.
The second eclipse completely nullified everybody's powers. It's stronger than the Haitian's power, as it reduced Daphne to a crippled state, while she was able to walk around the Haitian. Claire also started dying of common bacteria, due to not having an immune system from her Healing Factor.
Maya and Alejandro Herrera. The latter's power is the ability to cancel out the former's uncontrollable poison emission.
In The 4400, Jordan Collier's ability is to depower others by removing the promicin that gives them their powers.
In Smallville, blue kryptonite causes Kryptonian powers to disappear, but it needs skin contact to work. Red sunlight, magic, and various alien devices can also take away Clark's powers. This case is notable for having a guy who DID use it to lead a normal life. It later bit him in the ass.
Stargate SG-1 has the Anti-Prior device the team cooked up against the Ori. It emits an inaudible sound that makes Priors unable to use their psychic powers; however, both Damaris and Daniel Jackson/Merlin were able to overcome it given sufficient time.
The Rada'Han is a collar in Legend of the Seeker used to nullify a person's magical ability. In one case, it was used to prevent a cursed person from turning into a monster. The Pristinely Ungifted are rare individuals completely unaffected by magic. When one is first introduced, she is able to walk through what is, essentially, a magical minefield as if it wasn't there.
In Painkiller Jane, neuros can be rendered harmless by "chipping" them with a special gun that implants a control chip into the back of their heads, counteracting their abilities. It doesn't work on advanced neuros, though.
In Star Trek: Deep Space Nine, the Obsidian Order had a prototype device that would prevent a Founder from returning to their natural gelatinous state, with potentially lethal results for the changeling if the device is left on for extended periods.
One of Zin's fugitives used a ray gun style device on Cole in Tracker, nullifying his Cirronian abilities until Mel discovered she could power him back up.
The HERO system has a power devoted explicitly to this, called Drain, which reduces the affected power temporarily (or possibly permanently). There is also Suppress, which is similar to Drain except Drain "damages" a power or characteristic and it automatically heals over time, while Suppress reduces the power only as long as the Suppress is maintained.
In Dungeonsand Dragons, spell "Mordenkhainen's Disjunction" can strip magic permanently from magic items. Also fits this trope in that, if a spellcaster successfully strips the power from an Artifact-level magic item (which has very low odds to even work unless the character has an obscenely high caster level), the caster himself must make a saving throw or permanently lose all magic related abilities and spellcasting. Fail the saving throw, and absolutely nothing (not even somebody else casting the ultra-broken "Miracle" or "Wish" spells) can restore the caster's magic. And just in case you didn't think the rules were already stacked to tell you casting Disjunction on an Artifact is a Very Bad Idea, there's also a 95% chance that some god, demon or other ludicrously powerful being connected to the Artifact will show up to punish the caster.
Power Nullifiers are known as "pulsing" effects in Sen Zar, and they're even more feared than in most other games, because of Sen Zar's munchkin-friendly design.
* Lejendary Adventures. Morben's Supernatural Shackles would completely prevent the victim from using any kind of magic, including magical items.
In City of Heroes, the Bio-Energy Feedback Inducer is a power-draining weapon used by the "Sappers." It works by draining your endurance, which all powers need to operate. EMP and electrical powers can do this as well, but not drain you completely in a single hit like a Sapper can.
A recurring boss in Fire Emblem: Blazing Sword is a Magic Seal named Kishuna. As his class name implies, he negates all magic in a 15-space radius of himself. It's all he can do, but since his speed is insane it can take some time to kill him.
The skill "Nihil" / "Mikiri" in the Jugdral and Tellius sagas. In the Jugdral games, it nullifies all enemy Critical Hit-based, and Special Sword skills ; in the Tellius games, it negates all enemy Battle skills. The Tellius games have in addition the Skill "Parity", which has the same effect but extended to the Skill's owner as well, and also negates both the skill's owner and his foe's support and terrain bonuses.
Guilty Gear has Sol's headband. It's technically a Power Limiter, but it makes him so weak his fire magic is completely nullified. Unless he compensates with an artifact that boosts specifically fire magic.
In Guild Wars Mesmers can drain an enemies energy, interrupt spells that are being cast and even entirely disable spells from being used for a time.
all classes have some form of a silence or interrupt effect. The first prevents the target from casting any spells until it expires, the other interrupts a spell that's being cast and prevents them from casting any spell of the same "school" e.g. interrupt a fireball and it stops them casting any fire spell. Due the devastating nature of being locked out like this for many classes (shadow priests until recently had zero non-shadow offensive spells) the duration of the silence or lockout is measured in a scant few seconds.
Anub'Rekhan is a boss notable for having an area of effect and particularly extreme Power Nullifier. When he casts it anyone near is unable to cast any spell, use any ability, or even just use a normal attack.
In Tokimeki Memorial 4, the Skill "Heart Unlocking Technique" / "Kokoro no Kaijoujutsu" negates the girls' negative Skills, such as Satsuki's "Noble" / "Kouki", and Tsugumi's "Tsun" Skills.
In Neverwinter Nights Hordes of the Underdark there is a dungeon with an artifact in it that nullifies any and all magic around it. You are reduced to physical abilities, and your fancy weapons and armor are only as useful as the materials they are made of (i.e. loosing all +X enchantments and such, but retaining their basic values such as armor class and damage dice) and your potions are just colored water. For some reason it didn't stop the spiders from growing unusually large.
In BlazBlue, Hakumen's Nox, Ookami, has this ability, rendered in-game as being able to null out projectiles, and in-story as otherwise immortal characters (Namely Nu-13 and Terumi) don't want it near them.
Terumi: Hey, Hakumen, I really don't want you touching me with your Ookami, so how about we do this...
One Celica A. Mercury has the uncontrollable ability to neutralize all seithr in an area around her. As seithr is required to use all ars magus and ars armagus, as well as the Azure Grimoire, she functions as this around most entities. Ragna's right arm and eye go completely numb around her as a result; likewise, the aforementioned Terumi shits himself if he catches sight of her (at the end of his CP Arcade, he screams for Phantom to get him out of there).
Azrael, one of the three newcomers from Chrono Phantasma, is an interesting case in which he has a Power Nullifier on himself that he purposefully applied. The Nullifier in question, his Enchant Dragunov tattoos, is activated/deactivated at will, and comes in three levels, with the third level unleashing his true power. The reason for his willing restriction was to draw out the battles he engaged in since fighting at full strength meant opponents who died easily, thus ending fights too quickly.
In Prototype, Alex gets injected with a parasite by Specialist Cross that disables his flashiest powers, though he still has Super Strength, Super Speed and the ability to disguise himself. He then spends the next few missions working with another scientist on trying to get rid of said parasite, with the final result being that he managed to gain new powers when he comes back.
Pokémon contains several moves that can do this. Disable locks out the target's most recently-used move for a few rounds. Imprison locks out any moves the target shares with the user until one of them switches out. Gastro Acid completely locks out the target's ability (such as the Shadow Tag ability that makes Wobbuffet a Game Breaker) until the victim switches. Finally, Grudge is a Taking You with Me version of this trope - if the user dies the round it's used, the target loses all the use points for the attack that last connected.
In Dragon Age, the Qunari treat their mages (called Saarebas - "dangerous thing") even worse than humans (and that's saying something), using magic-nullifying collars to keep them in line. The collars are controlled remotely. Just in case, though, they still cover the mages' eyes and sew their mouths shut.
During the Mage Origin, Jowan, Lily and Mage Warden have an Oh, Crap moment when they realise that the reason why the Rod of Fire is not melting the lock of the Phylactery Chamber and neither mage can cast spells is because the Templars have carved wards into the door frame.
In Lost Magic, several Sages wield powerful magic wands that imbue the very essences of their respective elements, granted to them by the Creator in ancient times. The Diva of Twilight, rather than receiving any particular element, has the "Wand of Balance," which in her words, gives her "the power to quell all other powers." This sounds like a lame power in comparison to, say, giant firey explosions at will... until she uses it to nullify the magic of EVERY other Sage, steals their wands, and tries to reset the entire universe with them. Maybe she was just tired of being mocked for being the most boring Sage.
Dishonored has the Overseers, who wield special music boxes that prevents Corvo from using his powers. However, that does not stop him blowing their brains out.
in Xenoblade Egil has a device called the Apocrypha made in order to disable Shulk's Monado, shorting out its ability to damage his Face Mechon along with its other powers.
The Elder Scrolls III: Morrowind features a remarkably simple way to keep slaves from casting spells: locked bracers enchanted with a small but constant magicka-drain effect. It takes a while to fully work, but once the magicka hits zero it's not coming back up barring magicka potions or removal of the bracers followed by sleep. No magicka, no spells.
In Mario & Luigi: Dream Team, Antasma has the unique ability to separate Dreamy Luigi from Mario and imprison him within one of his Antasmunchies. This lowers Mario's stats and leaves him with only his basic jump attack, so freeing Luigi ASAP is in one's best interest, though locating him isn't always an easy task...
Gamma from Gunnerkrigg Court prevents Zimmy's powers from acting up (or at least lessens their magnitude) simply by her presence. But it doesn't work as well when she's asleep—and she's pretty much Zimmy's only means of controlling her powers. Antimony can play this role for Zimmy in a pinch, but she's nowhere near as strong as Gamma.
At least one Spellwolf from Dominic Deegan has shown the ability to cast the spell "Null Magic".
Phil in Yosh! is the Null - as well as being immune to magic (see Anti-Magic for that) he can stop magic from working entirely if he's close enough.
In Spacetrawler, the Ites are uniquely qualified for police work because they emit an anti-telekinesis field.
In Kubera, the Sword of Re is a god-level item designed to fight sura. It inhibits the regeneration of anything it strikes (specifically, it brings it down to normal human regeneration, which is basically nonexistent), from sura to gods, making them far easier to kill. While most sura and any god could easily wield the weapon, the problem is that it does the same thing to the owner as well, and the only way to give up the sword is to die. This makes it a perfect weapon for a human, but every sura who has tried to use it has inevitably died quickly and messily.
In the Whateley Universe, there may not be gizmos that work as power nullifiers (yet), but some mutants (such as Negator and Damper) have that ability. It does backfire somewhat against Tennyo, however, as she actually gets more powerful with her mutant abilities suppressed; she just starts using the power of the Class X Entity contained inside her.
In the Global Guardians PBEM Universe, Purge has the power to turn off metahuman powers (but not magic or powers gained through technology, while Scramble can cause metahuman powers to misfire and not work properly (though they do tend to still work somehow).
SCP Foundation's SCP-514. Whenever in contact with the pigeons' nullifying "aura", every weapon (bombs, guns, tanks, baseball bats, knives, etc) is rendered completely useless and are even destroyed after prolonged exposure. Even objects not designed to be weaponized like pens were rendered useless if used for violent intent. In addition, the pigeons' ability can completely suppress the negative emotions and intent of all sentient beings, no matter how violent, which makes the capture of SCP-514 nearly impossible.
Disruptions in Elemental Powers of the series' Benders occur during temporary meteorological events. Firebenders and Waterbenders draw their power from the sun and moon, respectively. When solar or lunar eclipse occurs, the affiliated Benders lose their powers for its duration. It's also possible to stop Waterbending for good by destroying the moon through its totemic spirit, (which, while easier then it sounds in this setting, is not a good idea, as it will enrage the moon's partner, the Ocean)
Badass Normal martial artist Ty Lee has learned to disable the Elemental Powers of Benders by striking Pressure Points to block the flow of chi (resulting in considerable pain for some of her victims). In the series finale "Sozin's Comet". Aang permanently does this to Ozai, using energy-bending he learned from a giant Lion Turtle.
The Leader of the Equalists, Amon, claims to be able to permanently remove bending, with the implication he uses the same technique Aang used. In actuality, he's using a form of Bloodbending.
There are two in Danny Phantom. The Specter Deflector wards off anything ectoplasmic, so if Danny were to turn into his ghostly Super Hero counterpart, he'd get a nasty electric zap. The other is the more straightforward version of this trope: the Plasmius Maximus, designed to nullify ghost powers for a good three hours.
In X-Men: Evolution, Leech's power extends to more than shutting down powers: it can shut down anything. When he used it to its fullest, a good chunk of the city lost power. Like movie Leech, he can also undo physical mutations, such as Spyke's permanent bone-armor vanishing, restoring his season one appearance until the effect ended.
The Powerpuff Girls features Antidote X, first appearing in "Slumbering With the Enemy". Mojo Jojo threw it at the titular superheroes in said episode to reduce them to normal little girls, though this obviously didn't affect subsequent episodes. The Movie reveals that it was initially created to get Mojo out of his One-Winged Angel form, though the girls briefly considered using it on themselves so they would be better accepted without superpowers.
On Buzz Lightyear of Star Command, Zurg manages to turn off Mira's powers by setting her in a box that disrupts her concentration whenever she tries to use her powers. Since concentration is required, well....
Feakins from the episode "Deadzone" exhibits some sort of Nanite deadzone around himself. If Rex is in too close a vicinity to him, his powers don't work.
An indeterminate variant is used by Lex Luthor on Lord Superman at the end of the Justice League two-part episode "A Better World". What exactly happened to his powers are unknown but he's at least able to be captured and detained by conventional shackles once it's been used on him.