Hard to work with, but great against vampires. There's even a certain basis in reality for this - garlic contains Allicin, a potent anti-biotic and anti-fungal agent. Remember that the original vampire myths described them as plague carriers instead of angsty nobility or teenage estrogen bait.
Batman: soaks his Batarangs in crushed garlic for dealing with vampires.
Blade: Blade's opponents are sent into anaphylactic shock by garlic based pepper spray.
Played with against non-supernatural opponents in the Roger Corman film The St. Valentine's Day Massacre: a croaky-voiced gangster (played by a young Jack Nicholson) notes the belief that the garlic he's rubbed his bullets with will poison the wounds— kind of strange given what's known now about garlic...
The Dresden Files: Try this for a cheap, effective vampire-slaying tool — paintballs filled with garlic and holy water!
Sabina Kane has a variation with bullets containing apple cider instead of garlic. Same basic idea, but in this setting vampires are weak to apple-related substances rather than garlic, due to having an ancestral connection to Lilith and the Garden of Eden.
Ultraviolet: Instead of putting it in bullets, they put it in smoke canisters. Minimal effect on troopies, knocks the "leeches" flat on their backs.
Forever Knight: In the episode "Hunted", a hunter shoots Nick with bullets stuffed with garlic.
Castlevania: The manual for the first game stated that Simon Belmont soaked his signature whip in garlic juice and holy water for seventeen weeks before assaulting Dracula's castle. This is kind of undone since one of the first powerups the game will give you after every respawn is a ball and chain weapon that replaces the whip, and retconned out almost entirely with the increasingly-complex history of the whip in later games.
Played with in Oblivion. One quest requires you to kill a vampire, and reading his diary indicates that he has a weakness to garlic. He's annoyed at the fact that he's the only vampire who possesses this weakness (so far as he knows), making him a walking cliche.
In Wario Land 3 and 4, one of Wario's forms is to turn into a vampire upon being bitten by a bat. One of the ways to turn back is to touch a hanging string of garlic bulbs. Depending on the situation, this may be good or bad.
Weapons made from religious relics or containing pieces of such are often used against supernatural foes, often in combination with special materials.
Anime and Manga
The Magdalene Order uses scripture-inscribed bullets laced with holy water as standard ammunition against demons. They also have a small number of bullets which use the power of one demon to blow up another, with near-nuclear effects.
The demon bullet was deemed a failure, however, another bullet called The Gospel is perhaps the most powerful anti-demon bullet around, which is described as "a magic bullet made of a rare kind of silver that's synthesized using alchemy which has a spell inscribed on it at an atomic level." The results are quite devastating.
Similarly, SOP for gun-wielding exorcists in Ga-Rei Zero- is the application of spirit water (sometimes via grenade) in addition to the aforementioned inscribed bullets. These elements extend beyond gunplay, notably with inscribed motorcycle wheels and a weaponized iron.
Hellsing: Alucard's bullets, like his gun(s), are made to order - each is made from the metal of a Lancaster cross that was specially melted down for the purpose. The fact that the rounds are also explosive-tipped helps as well.
He later receives a gun which fires Macedonium silver-jacketed bullets with blessed mercury (quicksilver) cores. Those don't need an explosive added, since mercury, being a liquid with about the same density as lead, virtually explodes upon terminal impact anyway.
Similarly, Father Alexander Anderson uses bayonets that have been blessed which causes instant death to the fake vampires and causes intense damage and pain to true vampires, if they try to remove the blade, they will burn themselves. He also uses pages of religious scriptures, in the TV version it prevents vampires from using their powers and in the OVA it simply creates barriers that vampires cannot cross.
Astro City: "Confession" story arc, a squad of alien invaders is armed with holographic crucifixes, restraining cables soaked in holy water, and a two-handed stake-launching revolver. They are thus armed because they know that the nocturnal super-hero Confessor is actually a vampire.
Constantine: melts gold from crosses to make shotgun shells.
He also blesses the water tank in a building's sprinkler system in order to spray all the demons there with holy water.
Dogma: Silent Bob kills the demon Azrael with a golf club he stole from a cardinal. As it turns out, the previous owner blessed it to improve his score.
Van Helsing: used a gas-powered fully-auto crossbow. It was only effective after dipping it in holy water.
Folklore and Mythology
In Swedish folklore, lead bullets are not only "lucky", they are also the only way to hit various supernatural menaces like shapeshifters, witches and their familiars, and animals protected by fairies. But it can't just be any lead; it has to be taken from a church window, which makes the making of the bullets blasphemy.
The Knights of the Cross each carry one of three swords: a broadsword (that may or may not be Excalibur), a katana, and a saber. Each sword has one of the nails used in Christ's crucifixion worked in the hilt. While Harry used to believe that the sword had little powers on their own, acting more as a symbol being powered by their wielder's faith, the swords have shown that they are more than mere pieces of steel.
It also provides us with an awesome vampire-slaying tool: a paintball gun loaded with garlic and holy water balls. It's up there with the stake machine-gun in Sluggy Freelance.
John Dies at the End: Dave and John use a Bible duct-taped to a baseball bat to fight supernatural monsters. Oh, and breath mints with the Lord's Prayer printed on them.
Felix Castor: Felix's landlord Pen fends off a succubus with a shotgun full of filed-down rosary beads. It seriously ruins the succubus's day.
In the Anita Blake books, in order to better kill vampires, Edward has been known to take a hollow point bullet, fill it with holy water and silver nitrate, and then seal it with wax.
George Macdonald Fraser's The Candlemas Road has an interesting inversion: a dying border reiver begs the narrator (a priest) to baptize his right hand. You see, his parents only baptized the rest of his body at birth: they wanted their son to strike "unblessed blows" (presumably in the hope that this would in some way damn his enemies to hell.)
In the Discworld novel Carpe Jugulum, we encounter Genre Savvy vampyres who have trained themselves to resist holy symbols. However, at one point, a vampire is beheaded with a holy item created on the spur of the moment due to the powerful faith of the wielder.
Monster Hunter International: Holy symbols in general work against undead and warding stones which specifically work against anything that's actually unnatural/eldritch in nature to the point of being an effective Fantastic Nuke. An actual bullet made of silver has horrible ballistics; so they get around this by by making hollow-point normal bullets with a silver ball (basically, a modified Corbon Pow'r Ball).
This one actually happened in the Middle Ages, with relics (bones and personal items from saints) being used in the ornamentation of swords and other weapons. They were intended to be "blessed" with special powers (notably less successful than in fiction).
Many weapons for dealing with the daemons, who, while not Immune to Bullets, are damn hard to kill. The most obvious are the psycannon shells used by the Ordo Malleus. Depending on the source, these are either filled with various blessed materials or have anti-daemon runes and prayers carved onto them.
Combining with Kill It with Fire gives flamethrowers loaded with Holy Promethium (napalm with the mystical properties of Holy Water). The Grey Knights' Incinerator is the best known example.
The Imperium also has special psych-out grenades that negate the Psychic Powers of those who are hit. It is said they are made using a material that is created as waste by the life support system of the Golden Throne and emanates negative psychic energy. Yes, The Emperor's shit kills psykers. He's thatBadass.
The forces of Chaos sometimes make use of daemon shells, which are bullets or artillery shells with a daemon bound within them. When the shell hits the target, the daemon's energy is released, causing a very large explosion of warp energy.
A Bo staff made from the largest known piece of The True Cross,
Sai made out of St. Peter's sword,
And bullets that had been in the Pope's mouth(wash).
Iron, often Cold Iron or meteoric iron, is a traditional ward and weapon against magic, especially The Fair Folk. The term "cold iron" comes down to us from folklore, apparently as a poetic form of words (much as "cold steel" was used in later times). In various fictions, the definition of cold iron varies greatly.
Elseworlds story Superboy's Legion: where Ferro Lad proves completely invulnerable to the Emerald Empress's magic.
In one Wolverine comic, the chestular protagonist is facing an opponent who is immune to any weapon forged by mortal man. He uses a weapon made of meteorite iron and forged by a demon to ruin said opponent's day.
Similar to the Ferro Lad mention, Colossus's organic steel body has caused difficulty to magical beings, including the Adversary, an entity claiming to be Baba Yaga, and the demon N'astirh.
The Saga Of Recluce: features two distinct types of magic: Order-mage and Chaos-mage. Chaos energy has difficulty working on iron due to the natural Order energy woven into it, making it a solid defense. Additionally, Chaos-mages tend to build up a large amount of the energy in their body, so direct contact with iron causes their skin to blister painfully, and in extreme cases can lead to death.
Redwall: Martin's ancestral sword is reforged by the badger lord of Salamandastron using meteoric steel in Mossflower. The same sword is used by nearly every protagonist and has always slain the Big Bad of each particular novel (though not always directly, sometimes it is just used to, say, cut a rope holding a giant bell directly above the Big Bad).
Discworld: any iron can be harmful to The Fair Folk (which makes Tiffany Aching's choice of a frying pan as a weapon an apt choice). However, some places are protected by a powerful magnetic field to keep any iron from entering. Nanny Ogg uses one of Binky's horseshoes, which can go anywhere (like Binky's Owner).
Considering an explanation, "cold iron" on Discworld is an overstatement and means just "below Curie point".
Born to Run: humans fighting The Fair Folk with, among other things, shotgun shells loaded with "Cold Iron, holy herbs, and blessed rock-salt." One character also has a seltzer bottle that's been filled with iron filings and given a "pagan blessing." When he sprays the blessed and iron-laced water directly into a banshee's mouth, its head melts.
Soldier Son trilogy: iron beats any kind of magic and mages are "allergic" to iron. At the beginning of the series, the protagonist's country Gernia has subdued most of the magic-using peoples around them by switching from lead to iron bullets.
Warlock of Gramarye series: iron in any metallic form is potentially deadly to the Little People. A handful of nails thrown into the bushes by a villain in one book is answered with cries of pain. And hanging scrap iron around your house also prevents the Wee Folk from entering. (The first book's claim that "witchcraft" (Psychic Powers) can't affect iron is RetConned away very early on).
The Spiderwick Chronicles book four: Jared confronts a faerie by pulling out a steel knife. His reasoning was that faeries don't like iron, and steel is at least part iron. It worked.
Anything with a high-enough iron content is potentially lethal to faeries; Mab, Queen of Winter and one of the most powerful magical beings on earth, recoils from a steel nail in fright the second before it touches her skin. Harry explains in one book that iron is to faeries what nuclear waste is to humans — horribly wracking, and to be avoided at all costs. He even takes down Aurora, the Summer Maiden and a powerful foe in her own right with nothing more than a fleet of pixies armed with box cutters.
Charity and her nail gun.
As long as they have iron, ordinary bullets do extra damage against the fae as well — even if your opponent is the size of a semi.
Steel Magic: modern day steel utensils (like forks) are effective against magical creatures.
The Witcher: the main character carries an iron sword that is quite effective against certain enemies.
In at least some versions of the stories, vampires are slain with an iron pike rather than a wooden stake, and/or iron filings may be placed under a child's bed to ward off vampires.
In folklore, wood stakes and iron nails are used to pin the vampire in its coffin (and then other things can be done to the body). It then dies and decomposes (and isn't coming back).
Changeling: The Dreaming: Cold iron (defined as "wrought iron") does aggravated damage to changelings... and if they die by it, their fae soul never reincarnates. The explanation is that the discovery of Iron working (and the coming of the Iron Age) was responsible for the end of the Fae golden age on Earth. Changelings, being creatures of dream and symbol, are especially vulnerable to it as a result. Later supplements explain steel not being so dangerous by the fact that it was invented by a powerful fairy long ago who sacrificed his life to insure it would be harmless.
Changeling: The Lost, "cold" iron (material that's 95% iron at least) pierces fae defenses and hand-wrought iron does aggravated damage to the True Fae. One of the explanations is that the True Fae made a deal with Iron to gain mystical benefits from it as long as they made sure no human hand could change its essence. Once humans discovered smelting, however, the deal was broken and Iron decided it wanted to do some interesting things to the kneecaps of the True Fae...
Hunter: The Vigil notes that the high-tech Hunter compacts and conspiracies, like The Cheiron Group and Task Force: VALKYRIE, occasionally use pure iron slugs in their guns when expecting fae activity.
Fair Folk take extra damage from pure iron weapons (not steel or other alloys), and are resistant to non-iron. Woe betide the Exalt who's stocked up on magical artifacts with no iron weapons.
There's a hearthstone called "Cold Iron Bauble" that can be mounted in said artifacts, which makes them act like iron to Fair Folk.
In Dungeons & Dragons, fae and Chaotic Evil demons usually have some measure of damage resistance that applies to all attacks, except for those made with cold iron weapons.
Princess Maker 2: adventure section of the game, there is an NPC Elf that can change your daughter's statistics. However, he will run away if your daughter is equipped with iron weapon or armor. It's surprising how the developers thought of this, especially when the game came from Japan.
Pokémon: The newly-introduced Fairy type is very clearly based on The Fair Folk. As such, one of their weaknesses is the Steel type, which definitely calls upon the traditional fae-repelling power of Cold Iron.
The Salvation War: gives us iron-tipped artillery in the form of High-Explosive Anti-Demon rounds. Normal High-Explosive-Anti-Tank (HEAT) rounds have a shaped charge with a copper liner so when they detonate they burn through the enemy armour with a jet of molten copper. HEAD rounds replace the copper liner with iron so instead of just burning through the demon like a HEAT round they burned through it with something that was poisonous to the demon and prevented its flesh from regenerating. Not that conventional (military-grade) firearms were any less effective against demons, over penetration of APFSDS rounds aside.
In Gargoyles, Xanatos tends to cut out the middle-man and have most of his weapons made of iron composites, just in case. Oberon may be a Physical God but even he takes major damage from anything forged from iron. At one (slightly depowered to impress his wife) point he is brought to his knees by Elisa Maza ringing an iron bell. In later episode he's toying with the main cast but finally decides to fight for real when someone impales him on a home-made harpoon gun.
Kryptonite and other Green Rocks
If the enemy is an alien or monster with a very specific, non-mythological weakness, be it Kryptonite, Music, or Water.
Anime and Manga
Cowboy Bebop: once featured a Creepy Child that was really a boy that stopped aging and gained ageless immortality from a weird cosmic event. A stone made during the incident was the only thing that could kill him and Jet and Spike carved it into a bullet to use it.
One Piece: Devil Fruit users are all weak to submersion in water (which is a pretty Weaksauce Weakness for pirates in largely oceanic world). Sea-Prism Stone is a rock that causes people touched by it to suffer the same effect as being submerged. Usually, it's used in handcuffs, restraints, and cages, but the marine Smoker walks around with a weapon made of the stuff despite being a Devil Fruit user himself.
In Smoker's case, it is only the tip of the weapon that has Sea-Prism Stone. Also, the Sea-Prism Stone only works when used in physical contact with the Devil Fruit user. A Devil Fruit user is fine inside the cage but as soon as they touch the stone, then they are weakened. Seeing as how the tip of Smoker's jitte doesn't touch him due the size of the weapon, he is fine and if it did brush against him then his clothes would protect him since it requires direct contact.
Tears to Tiara: has both the Holy Empire and the angels use weapons made of Electrum, a holy metal, against Noble Demon protagonist Arawn. (The latter made it the ammunition of a biological "divine tank", which was used killed him the first time). In-game, any equipment made of Electrum given to non-human characters (elves, dragons, demons, etc.) is only as good as whatever they were wearing earlier. It doesn't lower their stats, but it doesn't boost them either.
Superman: Kryptonite is Superman's one true weakness (usually), so it's hardly surprising that it's been weaponized against him. The most spectacular being the occasionally mentioned K-Bomb, a Kryptonite tipped nuclear bomb.
At the beginning of Final Crisis, Darkseid kills his son Orion with a time traveling Radion bullet — Radion being the one thing that can kill any New God no matter how powerful. Near the end of Final Crisis, Batman shoots Darkseid with the same bullet which jump-starts the latter's Rasputinian Death.
In an interesting inversion, Bloodscream seems to be able to recover from attacks by Wolverine's adamantium claws. Guess what happens when he faces Wolverine without the adamantium.
In X-Men Origins: Wolverine X-Men: Origins, Stryker manages to bypass both Wolverine's adamantium bones and healing factor by shooting him in the head with adamantium bullets. The bullets pierce his skull, and while Logan's brain can heal, his memories can't.
Battlefield Earth: the Psychlos are very resistant to damage due to their inhuman physiology, but anything radioactive would react explosively to the 'breathe-gas' that they used for respiration. In this case, the humans defeat all the Psychlos by simply detonating a nuclear bomb on their homeworld, and the destruction spread through their teleporter network. Though really, an ounce of plutonium in a lead box would have worked equally well.
Stargate SG-1: The mission of the entire SG project was to exploit alien technology or hybridize it with conventional weaponry to defend the Earth.
Gen. Vidrine: You're telling me that a slammer missile could take out a Goa'uld mothership?
Maj. Carter: When equipped with shield frequency modulators and naquadah-enhanced warheads... yes sir.
By the final season, they have bombs capable of destroying stargates, which are nigh invulnerable.
Also in this category is the energy weapon the SGC develops in SG-1 season 7 to kill Kull warriors.
Rifts: The New German Republic has discovered that hot uranium rounds prevent supernatural beings from regenerating or even healing damage.
Command & Conquer: both Nod and GDI use specialized munitions. In Nod's case, they have a love for filling missiles with various breeds of Tiberium-based explosives or gases, while GDI has developed sonic-based and EMP artillery shells and grenades.
Monkey Island series: root beer is an extremely effective ectocide. It only works on ghosts— when Guybrush tries this on the resurrected Zombie Pirate LeChuck, he shakes it off and chastises Guybrush for trying to off a zombie with a mere soft drink.
Super Robot Wars OG Saga: Endless Frontier: Though not particularly used against live targets, Haken's Night Fowl requires special bullets to destroy the Mild Keil crystals causing Broken Bridge antics and other chaos in-game. To ensure they're strong enough for the job, they're made from (or based on the composition of) fragments of the crystal type they're made to break.
Hunter: The Vigil: Task Force: VALKYRIE uses bullets treated with the power of SCIENCE! to turn them into super-high-energy rounds that can strike and harm incorporeal targets like ghosts.
Rage: Feltrite tipped bullets are more effective than lead, but rarer, more expensive and you are not able to carry as many of them.
Nobody Scores!: one of the characters acquires a hunk of Kryptonite and goes to sell it to Lex Luthor. Superman takes them out from long range with a traditional sniper rifle of his own before they even spot him.
When only magic can affect a monster, sometimes infusing magic into a more mundane weapon will do a better job.
Anime and Manga
Fate/Zero: Emiya Kiritsugu's custom "Origin Bullets" were filled with his own powdered bones, which contains Kiritsugu's dual Origins (base 'orientations' of an individual) of 'Binding' and 'Severing'. A magus uses magecraft to defend against the bullet? The Origins are forced directly onto his Magic Circuits, overloading them and ripping them apart.
The Nasuverse also contains "Conceptual Weapons", the highest class of offensive magical artifacts. One of the most powerful is a gun known as the "Black Barrel", which is specifically designed to kill immortal things, and becomes more powerful the more supernatural power its target possesses. In other words, it can One-Hit KillEldritch Abominations. The catch is that only an ordinary human can wield it: anyone with magical power finds it harmful to the touch.
Mahou Sensei Negima!: Tatsumiya creates her own spell-imbued bullets for exorcisms and the like. Later, she gains a special time-displacement rounds use within one day, which work as an effective One-Hit Kill for the ultimate in battlefield removal.
Outlaw Star featured Caster shells. Although the exact terminology fluctuated slightly depending on who was doing the talking (and who was dubbing/subtitling the episode), it all boiled down to "big ass guns that fired bullets which exploded into magical spells." The guns themselves were rare, but the more simple Caster rounds were relatively easy to find; when Gene needed to get the really good ones to take on the Big Bad he needed to track down the trio of semi-ageless techno-sorcerers that made them in the first place.
Hellraiser: In the "Razing Hell" comic mini-series, written by the Wachowski Brothers, the protagonists manage to make bullets out of some of their own bones (starting with a fallen comrade who tells them how to do it with his dying breath, and later, in one desperate situation, a character uses his own pinky finger to make more ammo), since one of the only things that can hurt the Legions of Hell is Leviathan's own power (which has tainted them too, since they were its prisoners). They use this knowledge to begin a grim but very effective La Résistance campaign against the cenobites and the puzzle-box guardians.
Superman: in the Silver Age Kryptonians could only be harmed by three things: other Kryptonians, kryptonite, and magic. So if you don't have any green rocks handy, get that Billy Batson kid to shout "Shazam" near him.
This is Played With in Kingdom Come, with Superman accidentaly cutting his finger while admiring Wonder Woman's magic sword. Possibly intended as foreshadowing for his later battle with Captain Marvel.
To take down Black Adam, a bullet was made from a piece of the Rock of Eternity
The Dresden Files: The enchanted silver swords the Wardens use can cut through enchantments and dispel physical attacks... as well as cut through nearly anything else (such as trees).
The Hollows: Rachel injects paintballs with potions, usually Sleepy-Time potions; they take effect on contact as opposed to ingestion.
Night Watch: it's very difficult for an Other to be killed with human weapons, as their instinct is to jump into the magical dimension of the Gloom at the first sign of danger, where physical objects cannot reach. Only enchanted bullets have a real chance of killing an Other. A human working for an Other is given enchanted bullets for his submachinegun. These bullets end up killing a werewolf. Besides that, only a nuke can definitively kill an Other, because nuclear explosions somehow reach even the deepest levels of Gloom.
Special Circumstances: Generally speaking, weapons imbued with the spirit of a member of the titular organization are often either the only way or the best way of slaying a supernatural beastie. There's also a discussion, at one point, of how normal, non-spiritual FBI agents could battle the supernatural, using "Cold Iron" bayonets for their rifles.
Tortall Universe: griffin-fletched arrows always hit their targets, and Stormwing-fletched arrows go through magic shielding.
GURPS Technomancer: The magical metal Necronium, is used primarily as a power source (and can sometimes poison those exposed to it and bring them back as the living dead), whilst depleted Necronium is toxic to all magical creatures. Depleted Necronium is also completely unaffected by magic, allowing it to penetrate nearly all protective spells.
Mage: The Ascension: Primium for the Technocracy, which is essentially a kills-supernaturals-dead weapon. Using it in a laser makes its wounds as agonizing to vampires as sunlight, Primium bullets hurt werewolves like silver does, and if you're afraid of magic users, plating yourself with Primium stops magic dead (some of the time at least.)
Mage: The Awakening: (the new World of Darkness's version of the above game) we are given Thaumium. It stores magical energy, it's resistant to magic, and it can cut through anything. Just for added punch, it's made from silver, gold, and mercury, all of which have to be mystically purified to produce the essential platonic essence of their being. Yes. Thaumium is made from a mixture of depleted precious metals.
Warhammer 40,000: Thousand Sons chaos marines use inferno bolts, bolt rounds infused with chaos power which can pierce power armour with ease.
Anything under rules with DR x/Magic (Damage Resistance of x points negated by Magic) will have a certain number of damage points deducted from any incoming non-magical attack. In extreme cases, a Redshirt Army's worth of mundane arrows will be unable to harm a monster. On the other hand, one Player Character using a magical bow to negate the resistance can defeat the same monster using the same arrows.
Earlier editions had numerous monsters flat-out immune to nonmagical weapons, or even magical ones below a certain threshold. The ability to hurt such otherwise "invulnerable" creatures was a major factor of what made magical weapons, even a lowly +1 sword, special.
Eternal Darkness: any weapon can be enhanced with magick. Imbued projectile weapons, including crossbows, rifles and shotguns, launch/fire imbued projectiles. It's not necessary to killing monsters, but sure helps.
Fatal Frame/Project Zero: the character is often an otherwise ordinary person who has the misfortune to "see things other people can't see", which inevitably leads to trouble when they stumble into the haunted house/village/island populated by the restless spirits of the dead. The main weapon used to fight these incorporeal nightmares? A camera. Yes, a camera. One which uses some sort of special crystal or mirror in its makeup so that the user can see ghosts, dispel mystical barriers, and drive off the dead with the snap of a picture.
Eternal Darkness: you can cast an enchantment spell on your weapon that can boost damage. If you use the alignment rune (IE: using the Xelatoth rune on monsters aligned with Chatturga), it boosts damage even more. Some weapons are firearms, especially in some of the levels based closer to present-day. Wanna plug a minion of an Eldritch Abomination with a WWI-era Enfield rifle imbued with the power of that Abomination's rival?
Biotics in Mass Effect aren't exactly magic, but they're close enough for government work, so Warp Ammo - bullets imbued with biotic power - would qualify. Warp Ammunition is a signature power of Jack in 2 and Liara in 3.
Silver weapons, including Silver Bullets, are commonly used on Werewolves and (less frequently) Vampires, stemming back to the idea of silver being a pure metal and/or associated with the moon. (Note that in Real Life, silver and copper do have biocidal properties. The idiomatic "silver spoon", as well as the common brass doorknob, is very effective at killing bacteria on contact. Silver nitrate is one of the oldest disinfectants, and one of the few such remedies still commonly used.)
Batman: One story note "written by Bob Kane" early pits Batman against a vampire, whom he kills (he did that back in the day) by melting down some silver candlesticks, forging bullets out of them, and shooting the vampire.
Fiends Of The Eastern Front: the main character melts down silverware and forges them into bullets for his machine gun to fight Constanta's vampire troops.
Blade: at least the film and TV adaptations, uses silver-coated steel in his melee weapons (spikes and swords).
Underworld: the vampires fight with bullets filled with silver nitrate note better known for its real world use in the eyes of newborn babies to prevent infection right after birth, and in photography. Considering how thick and silvery it is, one assumes this ammo is rather stale (silver nitrate looks like table salt, but gradually forms black deposits of pure silver over time, or more quickly when exposed to light).
In the movie ''Silver Bullet, Gary Busey forges a silver bullet from some necklaces to use against the werewolf. When the gun shop owner looks at him strangely, he tries to pass it off as "the kids really like the Lone Ranger." The other guy has a smirk that says, "Yeah, right."
During the climax of My Best Friend is a Vampire, a Vampire Hunter armed with silver bullets (played by David Warner) shoots the head vampire Modoc (played by Rene Auberjonois). The latter falls, apparently dead. In a minute, though, he gets up to the surprised protagonist and shocked hunter. When asked by the protagonist (an inexperienced vampire) why a silver bullet didn't kill him, Modoc reminds him that silver is for werewolves.
The Dresden Files tightens the qualifications by having a cursed werewolf note As opposed to one of the other three different kinds, which are all vulnerable to normal weaponry that can only be killed by inherited silver.
The Bartimaeus Trilogy: Silver is used as a weapon against spirits, since Silver actually causes damage to their essence, and can destroy them if given enough time. Iron also works to a lesser degree.
In Night Watch series by Sergey Lukyanenko, Anton sometimes carries a pistol filled with explosive silver bullets. Deadly against werewolves and low-level Dark mages. They aren't likely to kill vampires, but still hurt like a son-of-a-bitch.
In Monster Hunter International everyone uses silver in bullets, because it's the only thing that kills some type of monsters and generally has a stronger effect on many others. Theories why this is so are many, but no-one knows for sure. The exact method depends: pure silver is crap as a bullet, so many Hunters use a modified Corbon Pow'RBall design: Hollowpoint round with a silver ball. The US government agencies use a different design for their rifle ammunition.
In Abraham Lincoln: Vampire Hunter, President Lincoln, aware that vampire troops are fighting for the Confederacy, orders all the silver in the country to be melted down and turned into silver bullets and cannon balls.
Blood Ties: Detective Mike Sellucci is given silver bullets made for his police-issue Glock 9mm to kill a wendigo. He pumps it full of silver before the creature explodes.
In True Blood, the Fellowship of the Sun sent a suicide bomber whose bomb-vest was layered with silver shrapnel to attack a social gathering of vampires and friends.
In Supernatural, silver blades and bullets will dispatch zombies (reanimated by dark magic), shapeshifters, werewolves and more.
Doctor Who: In the classic series, the Cybermen's breathing apparatus intake was readily clogged by any gold which might accumulate there. Gold dust could be used to clog up the works if you could get your hands on it. However, the effectiveness of this weakness became Flanderized to the point that by the end, you had a handful of gold coins and a slingshot making a whole platoon of Cybermen a non-issue; when touched by gold they fall down screaming and sparking. When the Cybermen were brought back for the new series, they were an alternate universe breed who had the weakness dealt with in R&D according to a Freeze-Frame Bonus shot. However, a recent Cyberman appearance gives them some weakness to gold, though much much much milder than in the old series. (according to the writers, the two breeds have worked together for some time and this new breed that comes from that collaboration has aspects of both.)
In the manhua series ''Bloodline, the Shengdi use silver bullets as their main rounds. There are alos different kinds of silver bullets and one specific kind is capable of killing the main character.
Werewolf: The Forsaken: if silver touches a werewolf's blood, it burns them for aggravated damage and has a rare chance of messing up their Healing Factor. Unlike in Apocalypse, however, using silver on another werewolf is a major sin on the Karma Meter. It's also implied that the Pure get messed up worse than the Forsaken because they never sought forgiveness from Luna for the death of Father Wolf.
Hunter: The Vigil: even the lower-tech groups, are known to use silver bullets in their guns, though they don't always use them against the right enemies (i.e. werewolves).
Dungeons & Dragons: there are rules for coating any weapon with "alchemical" silver. This applies a penalty to using the weapon so many players will carry a silver coated sidearm. Magical weapons typically don't need coating.
Parodied in a Robot Chicken sketch: A werewolf is shown running from some kind of hunter and gets shot. The werewolf then claims "Only a silver bullet can kill a werewolf!". The hunter then proceeds to shoot the werewolf into a bloody pulp with a chain gun, light the mess on fire, snort the ashes, crap it out on a toilet and get processed in a sewage plant. Cut to 3 kids playing some sort of tabletop game, with the game master reading from the book and saying: "It says it's STILL not dead!"
A common way to kill vamps, using UV rounds, grenades, lamps, or other tricks. The implication is that a number of supernatural creatures are susceptible to ionizing radiation (by definition, light capable of tanning skin is ionizing), which is often used to sterilize tools and food, tying into the concept of supernatural creatures as plague carriers. It also means that someone should perhaps attempt to kill vampires with X-ray machines or plain 'ol depleted uranium.
Ergo Proxy: the only way to kill a Proxy is with shells that emit UV radiation, because the Proxies were designed to terraform the world back to normal and then disintegrate when the sunlight came back.
In Gantz Kei at one point uses a UV lamp to great effect against vampires.
Paralleled on occasion in some weapons against Superman developed from the spectograph of Rao (Krypton's red sun) which takes away his powers until he is again exposed to solar rays.
Notoriously used by the Soviet Union in Frank Miller's classic, Batman: The Dark Knight Returnsnote in which Superman took his devotion to Truth, Justice and the American Way to include enforcing US Policy abroad. who had tempered a high-yield nuke to do as much ecological damage as possible. Effects included a hemisphere covering EMP and a dust cloud that blocked out the sun in very literal nuclear "winter" way. Since Superman was trying to intercept and redirect the ICBM, it almost kills him because he is left with almost no exposure to his solar power source (he somehow drains energy from some plants to get back on his feet, but is still noted to be operating well below his peak power weeks later).
The U.S. military under General Sam Lane has been working on "black hole" technologies to fight Superman. These include "max-grav-photon-emitters", a.k.a. "black hole lasers", and "black hole bullets", which are 50 caliber rockets with light vacuums inside of them.
The Russian military has also been working on anti-Superman technology, specifically the "XR" drones. These unmanned drones have shielding that protects them from Superman's Heat Vision and Super Senses, as well as firing bullets that emit red sun radiation just before impact to be able to pierce Kryptonian skin and armor.
Blade: Has UV lights on his car and weapon-mounted tactical light. Hannibal King's guns shoot UV-radiating bullets.
Nightlife: a hematologist creates a "prison cell" for a vampire by strategically positioning ultraviolet lamps.
30 Days of Night: ultraviolet causes severe burns to vampire. Unfortunately the protagonists couldn't (or just plain didn't) use it effectively
Underworld: As pictured above, the Lycans go armed with bullets filled with a liquid that emits ultraviolet radiation. It works very well.
Van Helsing: had a full spectrum sunlight grenade. He didn't know what it could be used for, but he thought it would come in handy.
In Derelict UV crossbow bolts appear to be the protagonist's chosen weapon against her robed and masked enemies.
If the enemy, usually a vampire, is vulnerable to wood, the solution is to upgrade the stake into a wood tipped bullet or more powerful and faster reloading crossbow.
Blade:In his original comic book appearances, Blade used knives made from the hardest teak wood against Dracula and pals.
Folklore and Mythology
Norse Mythology: only mistletoe could harm Balder; everything else in the Nine Worlds had promised not to hurt him, because Balder was just so damn pretty. (The mistletoe probably would have promised too, but Frigga forgot to ask it.) Magnificent Bastard Loki simply could not resist the opportunity this presented...
Sherlock Holmes: wooden bullets were used to threaten the Count in The Holmes-Dracula File. The Count himself notes (either in that novel or in one of the others set in the same continuity) that wood is deadly to his kind while metal cannot truly harm them. This is, in fact, what he takes advantage of to fake his death at the end of The Dracula Tape, Saberhagen's take on Stoker's original tale, to throw his dogged pursuers off his trail for good.
Buffy and its Spin-OffAngel: both use crossbows, and Angel has two devices that extend stakes hidden in his sleeves. Connor also used an automatic-staker in his first appearance as a teenager.
A later episode of Angel shows that members of the Wolfram and Hart Spec Ops Team carry wooden combat knives.
In True Blood, the Fellowship of the Sun developed quite an arsenal of wood-tipped projectile weapons.
They're not the only ones. When Bill decides to kill Sophie-Anne, the Vampire Queen of Louisiana, he brings in a whole SWAT team armed with assaut rifles with wood ammo. Even an experienced and powerful vampire like her can't do much against More Dakka of wood.
Wood is used against vampires all over The Vampire Diaries, in forms ranging from a standard hand-driven stake to a crossbow to wooden bullets that can be fired from a standard pistol. The wooden bullets aren't enough to kill; however, the homemade stake gun is.
The paramilitary vampire hunters in Ultraviolet use charcoal-nosed bullets.
Rifts: has wood-firing railguns (with embedded metal cores for the magnets to work on) on occasion for dealing with vampires. It also has actual depleted uranium shells (Not quite depleted, as these were described as still being more radioactive than normal DU rounds), which for reasons unknown retard magical abilities to heal. These are great for those pesky critters that fight you down to their last MD point and then teleport off and return an hour later fully healed, giving you the time to hunt them down and finish the job. There are also shells made of non-depleted uranium that actively interfere with magic use by anything they embed in. Both can be cured by physically removing the round, however digging into your side with your own claws is generally A Bad Idea.
Sluggy Freelance: Riff comes up with this baby. Too bad it only holds one second's worth of ammo and takes two days to reload.
Everything at Once
For weapons that combine various weaknesses into one shotgun shell, sword, or what have you. Just to cover all the bases.
Astro City "Confession" story arc (see above): Mordecai Chalk, a cyborg monster-hunter. He had a shotgun that fired shells with wolfsbane and holy water, mechanical parts etched with holy symbols and crafted in iron and silver, and an on-board computer that references thousands of occult tomes. It doesn't do him any good.
In When Titans Clash by Tenhawk, the Knighthood used counter-supernatural artillery rounds that were "... based around a core of three kilos of military grade high explosive which was surrounded by a sphere of blessed silver segmented into frangible pieces approximately one cubic inch in volume. This was in turn surrounded by pure meteoric iron in a second sphere, segmented into similar pieces."
The titular character of Hellboy fights most demonic creatures using a big honking gun (forged from a church bell, no less) with ammunition comprising of glass bullets filled with "holy water, clover leaf, silver shavings, white oak... the works.".
Discworld: In the undead bar of Ankh-Morpork, the bartender, Igor, has a weapon as follows:
"Like many barmen, Igor kept a club under the bar to deal with those little upsets that occurred around closing time... Igor's weapon of choice was a little different. It was tipped with silver (for werewolves), hung with garlic (for vampires) and wrapped around with a strip of blanket (for bogeymen). For everyone else, the fact that it was two feet of solid bog-oak usually sufficed."
Star Trek: The Next Generation: "Greater Than the Sum" introduced a "multivector weapon" designed to use everything against the Borg that had ever been somewhat effective. Then the Borg got ahold of it before it could be used against them—and did what they always do—they adapted.
The Bartimaeus Trilogy: All spirits from the weakest mite to the greatest marid can be severely hurt by silver, iron, and certain types of herbs and spices, such as rosemary. Magicians, commoners, and other spirits exploit this to no end. It gets to the point where powerful spirits are taken down by improvised use of everyday metals more often than they are by the devastatingly destructive spells these entities can employ.
Reserved For The Cat: the heroine carries a revolver loaded with two Cold Iron bullets, two Silver bullets, and two Blessed Lead bullets, plus extra ammo of all three types. It's anyone's guess which type offed the mystical Big Bad at the end of the novel.
Supernatural: the hunters have to improvise a variety of weapons to kill a variety of creatures. The hunter's arsenal makes use of most of the above, exceptgarlic. The most frequent example is their use of shotgun shells loaded with rock salt against ghosts. Ghosts cannot act on iron, and are killed when their remains are salted and burned. Bobby's saferoom is walled with Iron treated with rock salt. Holy weapons can be found with holy water, which cannot be crossed by demons, or holy oil, which cannot be crossed by angels. This has even been weaponized into a molotov cocktail. Angels also can be killed by And when all else fails, there's a magical gun and knife that kill everything. Except when they don't.
The alpha shifter proves vulnerable to iridium.
The general method seems to be - if it's a demon, apply holy water followed by magic knife or exorcism (if you have time). If not, apply iron, silver, and liberal amounts of salt (often loaded into shotguns) and fire. All that said, the one thing that seems to have been capable of taking down anything a hunter faces (with a few exceptions) is relatively mundane - beheading. It's the only way to kill a vampire (aside from the Colt). Okami are susceptible to being run through a wood chipper. Wood chippers pretty much trump...everything. Presumably, they would work on a fair amount of monsters but the Okami is the only one ever shown in the show.
City of Heroes: this may be the only explanation for heroes with assault rifles being able to take anything down at all. Unfortunately this works the other way, too, as mooks and bosses of a high enough level can worry heroes protected by magical forces, power armour, and the like with ordinary guns.
Dungeons & Dragons: includes a plethora of monsters with varying types of damage reduction, such as werecreatures, demons, fey and others, which often results in adventurers carrying around extensive collections of weapons ("No, we need a silver magical weapon that does piercing damage, not a cold iron one!"). Both melee weapons and ammunition for projectiles are often made from these special materials.
An insanely genius item introduced in one of the Van Richten's Guides was a weakness-detecting arrow. Rather than a traditional point, it had needles from over a dozen different substances, like cold iron, gold, silver, wood, and so on. When fired, it does minimal damage to its target, but also does not embed itself. After it is recovered, the wielder can see what substance did the harm based on which other needles are broken or bent, and (depending on the target) which needle has the blood stain.
Epic-level monsters (i.e. challenges for level 21+ characters) sometimes require truly bizarre weapons to deal normal damage to them. A time-elemental Phane can only take normal damage from weapons from an alternate history, for example, and a mind-consuming Dream Larva only takes real damage from weapons forged by a sleepwalking blacksmith.
The Regeneration Ability that stops a creature from being killed by attacks that do not overcome it. For example trolls can only be killed by fire or acid damage.
There are magical weapon enhancements that can compensate for the "golf bag scabbard" problem. Metalline weapons overcome any damage reduction based on the material composition of the weapon, Transforming weapons can change shape into other types of weapons which deal damage in a different manner (bludgeoning, piercing, slashing, or some combination), and Shadowstriking weapons can temporarily attune themselves to a particular creature and overcome whatever damage reduction it happens to have.
In the Dresden Files RPG, many types of supernatural creature have a power that improves their toughness and/or regeneration. Every one of these is required to have a "Catch" or critical weakness, which will prevent their durability or recovery from taking effect. Catches are rated on a points system (helping to offset the cost of the original powers), with more common weaknesses providing a bigger refund. For instance, a creature that's weak against fire or sunlight gets a 4-point discount, because this is well-known and easy to find; one vulnerable to something more esoteric like True Love might only get 2 points, and someone vulnerable to only a specific, difficult-to-find object (such as the Noose of Barrabas) gets nothing. However, certain rare artifacts and powers allow a player to spend a fate point to simply declare that their next attack matches a given target's Catch, allowing them to penetrate whatever supernatural defenses it might have.
Parallel Dementia: Fall and other Nightmare hunters use blessed weapons (to combat demons), obsidian (for angels), garlic (for undead), iron (for fey), amethyst (for spawn), and silver (for therians) to combat the various types of Nightmares.
On at least one occasion, Fall is given specially made ammunition incorporating all of these at once, because she's about to head into an extremely tense situation and standard operating procedure (using a test clip loaded with one of each kind of ammo, in a specific order, so that you can switch to full clips of the appropriate variety when you find the one that works) would be dangerously time-consuming.
The legendary Usenet poster 'Gharlane of Eddore' once proposed a design for a Standard Generic Monster Load, which was:
Silver bullet; hex-scored jacketed hollow-point filled with a gel made of Holy Water, wolfsbane, garlic, fugu toxin and curare, laced with dimethyl sulfoxide to provide tractor-solvent Spreading Factor. Traditionalists can also cut crosses in the bases of the bullets, and have them blessed by a priest. .44 magnum 240-grain load over the standard Elmer Keith hunting load, 24 grains of IMR 2400 (the manual says 21.8 grains is maximum, so don't use the 24-grain load if you have a cheap revolver). These work reliably on Vampires, Werewolves, the generic Undead, and Evil Human Minions like Renfield, with sublime indifference.
If bullets won't kill it, then obviously the answer is to make better bullets. If they're just really well protected, use a harder material like bronze or tungsten. If somebody's playing tricks with magnets, use compressed plastic. With magnesium, you can Kill It with Fire! Or perhaps you can recycle their phlebotinum and Hoist Them By Their Own Petard.
Anime and Manga
Sven from Black Cat packs an array of interesting bullets, and among these there are blue-tipped ones that freezes the opponent on contact.
Kittan in Tengen Toppa Gurren Lagann at one point attempts to hold off a Mugann with a shotgun packing "Spiral shells." A more impressive one is issued to Grapearls, producing huge explosions and a shell to contain the aftermath of a Mugann going blooie.
X-Men: Magneto, Master of Magnetism is often faced with plastic or composite weapons, and was locked in a "plastic prison" on more than one occasion.
In the original animated series a Sentinel boasts about how its plastic coating stops Magento's powers... Magneto's response is an annoyed "You fools, this whole ship is my weapon! and promptly throws the huge generators nearby through the Sentinels.
The Mighty: Gabriel Colewas given some special bullets. It turns out that it's Special condensed nitrogen bullets to use against the invulnerable Alpha One since he needs to breathe more oxygen than most people.
The Daximites, a race of aliens which has Superman's powers, only weakness is LEAD, which means that any attempt to take over the Earth while firearms and lead bullets are the most common weaponry on the planet is pretty futile.
Transformers: The "6000-degree magnesium burn" of "high-heat 105mm sabot rounds" fired from an AC-130 gunship allowed the US military to hurt the marauding Decepticons in the movie (it's not much, but it worked rather better than normal bullets). Discarding-sabot rounds being neither hot, magnesium-laden or used by AC-130s, this has little to do with military practice or actual physics, though it is implied that weapons technology in the movie-verse is different because many human technological advancements came from studying Megatron's body.
By the second movie, the human NEST teams are shown carrying heavily-upgraded, large-caliber assault rifles and machineguns that can actually inflict damage on Decepticons; the NEST units and Marines fighting the Decepticons at the end of the movie prove surprisingly effective against the Decepticons in the all-out battle that results.
By the third film, a number of a key Decepticons are taken down without any help from Autobots beyond training shown earlier in the film.
In Posse, Jesse Lee has some of the stolen gold recast into golden bullets he intends to use on his father's killers. Father Time explains that, according to New Orleans voodoo ladies, gold is the only way to kill a demon. In Jesse's case, the demons are symbolic rather than actual.
The shells for the Götterdämmerung's main gun in Iron Sky are said to be made from metastable metallic hydrogen.
HammersSlammers: there's all sorts of strange weapons and ammo. One example is the "osmium penetrator" used by some of the other merc companies. These weapons take a rod of osmium, put behind it roughly a liter of propellant, and force it down a diamond-coated barrel to flechette thickness. It emerges as an osmium needle well capable of getting through tank armor, though it has little effect on personnel (the needle just blasts through people as if they weren't there, and since it doesn't splash, it just makes a very small hole). And powerguns, that fire bolts of energy from polyurethane wafers as ammo.
The Dresden Files: Kincaid at one point uses Dragonsbreath shotgun rounds to turn his disposable shotguns into flamethrowers. This inspires Harry to read up on other unusual shotgun rounds, including flares.
Dresden also keeps around some actual depleted uranium, in powder form, because it apparently has spiritual as well as physical weight and can dispel ghosts.
The Alloy of Law: Anti-Allomancer rounds. The expensive ones are made out of Aluminum, the cheap ones vary based on target: Coinshot rounds are fronted with ceramics that will keep going when they push on the metal, Lurcher rounds contain ceramics surrounded by metal and fragment when pulled, Tineye rounds are excessively loud, Thug rounds are enormously over-sized.
In Sergey Lukyanenko's Night Watch, most of the stuff mentioned above is useless against vampires (in fact, they deliberately let Muggles think it works). Even silver doesn't kill them (but being shot with a silver bullet hurts like hell). What's deadly against a vampire? Vodka. Luckily most of the novels take place in Russia, where vodka is everywhere.
Doctor Who: UNIT's final appearance in the old version, following an absence of some years, it was shown that they had got tired of facing Immune to Bullets menaces and developed special bullets to even the playing field. These included teflon-coated armour-piercing rounds for robots and Daleks ("A non-stick bullet?" the Doctor muses), high-explosive rounds for Yetis, gold-tipped bullets for Cybermen, and silver bullets just in case. The silver bullets turn out to be very useful.
This continues in the new series, where UNIT uses rad-steel coated bullets to counter the Sontarans' anti-bullet field (that expands the copper casing of normal rounds and stops the guns firing).
In "Revenge of the Cybermen", the Doctor mentions the "glittergun", which turns Cybermen into gold-plated statues as it clogs their vents.
In Kamen Rider Kuuga, a particularly persistent Monster of the Week (introduced in episode 2, finally offed in episode 39, though he doesn't appear in every episode) winds up getting its corpse analyzed to create special ammunition that can actually affect Grongi.
In Kamen Rider OOO, Kamen Rider Birth uses a gun which fires Cell Medals at Yummies. Given that the term phlebotinum seems to be a play on phlebotomy (drawing of blood), and that Yummies (and the Greeed who created them) tend to "bleed" Cell Medals, this seems to be a fairly direct invocation.
At one point in V: The Final Battle, the heroes discover that Visitor body armor is now impervious to conventional bullets. Teflon-coated bullets solve this problem rather quickly.
In the Star Trek: Enterprise episode "Regeneration", the Borg adapt their force fields to block Earth Starfleet phase pistols after a few shots. The Enterprise's engineers manage to boost the weapons' output, making them effective again ... temporarily.
The alien mechs in Falling Skies can't be damaged by conventional bullets. Bullets made from salvaged mech armor, however, are quite effective
Warhammer 40,000: has several examples, like Hellfire rounds, shells filled with a mutagenic acid that causes a near-instant and very painful death to anybody unfortunate enough to get hit by one, Dragonfire shells, which explode in a burst of superheated gas and Kraken bolts, which contain cores made of Thunderbolt Iron.
GURPS Ogre,: the standard anti-personnel round is "ap-fizz dizzy-doo" (APFSDSDU): armor-piercing, fin-stabilized, discarding sabot, depleted uranium.
Resident Evil 3: Nemesis: in addition to normal grenade rounds, also has acid, fire, and ice grenades. Code: Veronica also features anti-BOW gas rounds.
While we're on the Survival Horror note, the tail end of Parasite Eve features bullets laced with the protagonist's mitochondria. And that's not even touching the fact that the game's main feature is elite gun tweaking to make bullets that freeze, burn, tranquilize, or poison with acid and cyanide. (Then there's the crazy things the guns themselves can do, barring the already-powerful-enough rocket launchers.)
Chex Quest: Originally the flemoids/phlemoids (Whichever you prefer) were immune to conventional weapons. However, the "Zorcher" works by remodulating the dimensional frequencies of the creatures, sending them back to whatever realm they came from. Therefore, no killing the... green... slimy mucus things that want to eat the main character alive, and Ta-Da! It's kid-friendly!
BioShock: has ammo for weapons ranging from (relatively) realistic things like armour piercing bullets to things like electric shotgun shells, exploding shotgun shells, a flamethrower that also fires liquid nitrogen and electric gel, and a crossbow with fire bolts and bolts that shoot wires. And then there's plasmids...
Stars!: has depleted neutronium ammo — presumably, dense far beyond the bounds of normal matter. (How you deplete neutronium is unknown to modern science.)
Jagged Alliance 2 v1.13: introduced AET (Advanced Energy Transfer) ammunition. They pierce armor better and do more damage than standard AP rounds although less than hollow-point rounds when they strike flesh. Their price is huge and they also wear off guns faster then normal bullets. The developers suggest not thinking too hard about how that works.
Singularity: is powered up with the time-warping abilities of "Element 99." Some of the weapons have special abilities because of this (like a sniper rifle that slows down time so you can shoot a moving target) but for most, it just makes their bullets hit harder.
Ninja Gaiden: when Ryu used APFSDS cores as arrows, to destroy heavily armored tanks and helicopters. But then, that whole section of the game is an exercise in Refuge in Audacity. There are also explosive arrows for when getting through armour is less important than AOE.
Railgun rounds in Escape Velocity Nova are stated in flavor text to be forged of metals that are highly conductive but cheap, such as copper and gold. The rounds come in 100, 150, 200, and (with the ARPIA plug-in) 400 millimeter sizes.
The Godfather 2 has incendiary rounds as a reward for completing a certain crime ring.
In X-COM 3: Apocalypse the ultimate anti-alien weapons are anti-alien toxins and anti-alien gas. The former requires a special pistol and has to be upgraded twice to be effective against advanced forms, the latter is discovered fairly late, but can be used in grenades and missiles for existing launchers. Both completely bypass aliens' force field shields and pose almost no threat whatsoever to allied forces in the event of psionic attack. With those the last missions are a breeze. You still need conventional weapons, explosives or rayguns to disable alien structures, though. Good thing you can borrow them from dead aliens.
Equally, it takes multiple disruptor blasts or devastator missiles to take down your troopers at that stage, thanks to your Nigh Invulnerable disruption armour and stolen shield technology... and then the aliens bust out their enzyme guns, which shoot target-seeking organic 'missiles' loaded with nasty stuff that can melt through your super-armour in seconds. They may still be stopped by shields, but the moment you see them on the field, you take notice.
In Centurions, energy specialist Rex Charger had assault weapon systems that fired missiles that contained... energy-changing stuff. Magnetic shields, light, energy that was absorbed by a gun—the missiles were Technobabble shells. This meant that they were exactly as powerful as the plot demanded: on separate occasions, Rex blew up a Swirly Energy Thingy and killed a black hole.
In the My Little Pony: Friendship Is Magic episode Equestria Games, the final event in the games is an archery contest. The twist is that the arrowheads freeze what they hit, and the goal is to cover the entire target in ice before the other ponies. Chaos ensues when one participant trips up and fires one into a cloud, turning the entire thing into an ice ball which nearly crushes the audience.