Evil creatures are repelled by a holy object of the faith they believe in/used to believe in/are associated with. (A Jewish vampire is repelled by Torah scrolls, but laughs at crosses.)
You repel creatures by using a holy object that you believe in. (If you're Hindu, your shrine to Ganesha repels all kinds of evil things, no matter what faith tradition they come from.)
One symbol in particular is effective, or the symbols of one particular faith. (For example, crosses hurt vampires, period.) This might be because one faith is objectively correct, it might be for some other reason, or the characters may not know what the reason is—but if you want to scare off evil, that's the symbol you use.
Alucard from Hellsing has holy silver crosses melted down to make his vampire-destroying bullets. And then there's that one time where he can't be bothered to wait for the melted silver to be cast into bullets...
Alucard himself is affected by stuff of this nature (most notably Anderson's blessed blades), but is so ridiculously powerful that he can generally shrug it off.
In Chrono Crusade, demons are weak to holy water. The bullets in Rosette's guns "use holy water instead of an explosive charge," and in the anime Chrono burns his hand once when he attempts to use it against a demonic enemy.
The protagonist of My Balls encounters a succubus posing as a nurse, and tries to scare her off with a cross improvised from a scalpel and his own erect penis. It doesn't work.
In Digimon Adventure, Angemon's "Heavenly Knuckle" ("Hand of Fate" in the dub) attack completely annihilates Phantomon, and brings Vamdemon/Myotismon to his knees (Made even more impressive by the fact that Angemon was a whole level below the two of them).
Holy water acts like acid to demons in Ao No Exorcist, so it also affects the half-demon main character. This leads to a rather amusing scene where the Exwires are soaked down with the stuff to protect them, and the person doing the soaking very purposefully avoids Rin, awkwardly explaining it as "He's allergic to holy water." Which, technically speaking, is true, but...
In High School DxD, holy water and crosses hurt demons, as does prayer. Issei accidentally damages himself when he tries to chant a Buddhist mantra, and Asia often damages herself by praying to God. In fact in the Phoenix arc, this is Issei's trump card against Riser, using a cross and holy water to boost his attacks to nullify Riser's regeneration.
A slight variant is used in Marvel Comics with their vampires, in that a given holy symbol must have faith behind it. In one memorable exchange, Wolverine tries to use an impromptu cross to force Dracula to back off, who replies with something to the effect of "You idiot, you don't believe, that can't hurt me." Cue Nightcrawler, a devout Catholic, who jumps in and declares, brandishing a cross, "But I DO believe!" And Drac does the usual fall back, hissing schtick.
You can use any holy symbol you believe in. The symbol even works without any conscious effort on your part. In the same storyline, Kitty Pryde tries to drive Dracula back with a crucifix; it fails miserably, since she's Jewish. But when Dracula grabs her throat, Kitty is surprised to see his hand burn—from contact with the Star of David pendant she wears.
Marvel also has it only work if it is a symbol of a god worshiped in the time the vampire was alive. The first vampire, Varnae, can't be hurt by crosses, for example, because the crucifixion didn't happen until he was over 16,000 years old.
Marvel also has it that vampires can actually successfully use holy symbols against other vampires (who better than a vampire to know in the power of faith). Dracula himself once drove off a group of vampires hunting him with a large cross, and only suffered minor burns while flying for hours in bat form carrying it to chase them off. This might be a case of 'God was nice', as Dracula had to immediately drop the cross near morning, once the threat was over and he was no longer accidentally protecting a young human female and realized he was holding a cross. Obviously, this is an extremely rare deal.
In one issue of Fans!, idealist Trekkie Rikk is able to hold off a vampire with a Vulcan salute.
Subverted later, when the vampire shows up elsewhere and admits he faked it to shake off Rikk and his friends.
In Hellblazer, John Constantine makes brilliant use of this by sharing a drink with the Devil — and then disrupting a spell that keeps the liquid from reverting to holy water. He then glasses the Devil in the face with a broken bottle and kicks him into a well full of the stuff.
In I Am Legend, the "vampires" are only hurt by holy symbols if it was symbolic of the religion they followed in their previous life. For example, a former friend of Robert's is undeterred by a cross, yet recoils when presented with a Torah.
The Simpsons Comic: Mr. Burns takes over the Springfield church, at first simply to promote his autobiography and later to become Pope (yes, Lovejoy explains why he should have thought that through). He compares the Church to a book club where they talk about the same book every week. "Now, the Bible is a fine book, but - AGH! It burns!" In the next panel, he's holding it with oven mitts.
In Return to Prince Manor Snape possessed a Staff of the Magi given to him by Father Christmas which had the ability to repel evil. A dire wolf bit the staff instead of Snape's arm and got its mouth burned.
My Little Castlevania has the Golden Cross given by Aeon to the Mane Six and wielded by Fluttershy. It wards off all of Dracula's monsters (the Behemoth actually runs to its death trying to avoid it), and when Fluttershy panics and thrusts it into Marble's face, it leaves a cross shaped burn on her cheek.
In the Empath: The Luckiest Smurf story "Smurphony Of The Night", a Smurf head symbol is treated as a holy symbol by Empath when he uses it against the vampire Lord Vladimir Smurfula.
In Hocus Pocus, the witch Winnie sneezes, prompting a passing-by girl dressed as an Angel (it's Halloween) to say "Bless you!" All three sisters react with terror.
Subverted in The Devil's Advocate when the Big Bad sort of exposes himself by immersing a finger in a church water basin (along with an Aside Glance). The water boils, but the Devil is rather more amused than hurt.
Played with in The Dead Matter. Vellich has this reaction to holy symbols through and through, particularly when he dies by shoving a cross down his throat, but the drug the "new" vampires are taking allows them to be immune to both faith symbols and sunlight.
In Santo En Atacan Las Brujas, the mere sight of a large cross wielded by the heroic Masked LuchadorEl Santo is sufficient to cause all the titular witches to burst into flames. Earlier in the film, Santo is able to make some of the witches' wrestling minions flee by simply standing with his own body in the shape of a cross in front of a light source.
Subverted in The Fearless Vampire Killers when a Distressed Damsel holds up a crucifix to ward off a vampire, only to be told, in a heavy Yiddish accent, "Oy vey, have you got the wrong vampire!" Apparently holy symbols only hurt if they were ever holy to the vampire.
The song about Freddy Krueger from A Nightmare on Elm Street implies Freddy can be affected by crucifixes ("Five, six, grab your crucifix"), but no one actively tries to use them to repel him, though they do seem to make him nervous. In the third movie, holy water and a crucifix were used to kill him off at the end, however. Justified as his power comes from a trio of Dream Demons, and considering he feeds off of fear, having faith he can't hurt you if you have one probably would protect you from him.
Zigzagged in Warlock. When Warlock's Dynamic Entry into a priest house makes a crucifix fall from the wall, the first thing the villain does is pick it up and hang it back on the wall. However, he cannot step on holy ground.
In Stephen King's vampire opus 'Salem's Lot and its miniseries, this happens when vampires are touched by holy water, any crucifix, or any cross-shaped object that has been blessed. Father Callahan even burns his hands on the front doors of the church when he has been turned by Barlow.
Interestingly enough, the symbol itself doesn't seem to be explicitly needed. If Father Callahan had showed his faith by throwing the cross away as he agreed, the vampire wouldn't have been able to touch him. Since he lied and refused to throw away the cross, it lost all effectiveness, allowing the vampire to turn him.
In Star Wars, the ability Force Light banishes darkness around the user, and even has the potential to sever the connection of Dark Siders and the Force.
In The Silmarillion, the Silmarils, as pure and holy objects containing the light of the Two Trees, burn anything evil. When the villainous werewolf Carcharoth swallows one, the pain causes it to go insane. Similarly, when Anti-Villain Maedhros and Maglor finally manage to recapture them, after spending the entire book trying to kill anyone who has one and steal it back, the Silmarils burn their hands. This causes Maedhros to commit suicide and Maglor to wander the shores of Middle-earth forever in self-imposed penance. A Silmaril also burns Big Bad Morgoth for life and robs him of his ability to change shape.
Winds are also often seen to have effects similar to this in Tolkien's books (since wind is controlled by Manwë, holiest of the Valar), most notably in dispelling the darkness cast out from Mordor over Minas Tirith, and in actually dissipating Sauron's lingering spirit.
In Scott Westerfeld's Peeps, the hunters refer to the fear of an object that occurs as an Athame. The vampire-like infected hate things that they used to love. So in older times, when people were generally more devout, many vampires were warded off with holy objects. In one of the first encounters Cal has with a peep in the book, he uses a picture of Elvis as her Athame.
In Good Omens, Crowley kills the demon Ligur by dumping holy water on him. It's Crowley's weakness too, as he's also a demon, and that's why he is extremely careful handling it.
In Never Ceese, the Christian vampire and werewolf novel (No, really!), vampires and werewolves are cursed so that they react poorly to anything related to God or Christianity. This includes the typical weaknesses, as well as feeling sick when they quote or even think about scriptures.
In Kristine Kathryn Rusch's Fey novels, holy water dissolves Fey. Even a cloth that's been stored close to some holy water turns out to be a slow killer. The twist is that holy water is only deadly to fey because a human who was desperate for a weapon threw some at an attacking fey, and inadvertently used a forgotten magic to transform it into a weapon that would only work against them.
The Betsy the Vampire Queen series by Mary Janice Davidson has vampires vulnerable to anything holy, even holy names. Say "God" in front of one and he'll recoil. Covering their ears doesn't help, as the words worm into their psyches.
The Black Court (undead vampires) have all of Dracula's weaknesses, so they react to sunlight, holy water, and garlic. Religious items' power against vampires is based on faith; Dresden states that a cross would be useless in his non-pious hands, while a pentacle can channel his faith in magic.
Similarly, the Red Court vampires (whose real form is some bat-demon beast) are weak against symbols of faith.
Averted with those possessed by Fallen Angels. They may enter a church without any issue. This is possibly justified, as God doesn't want them destroyed, but for them to see the error of their ways and come back to Him. They still don't like entering churches, though, since it reminds them of what they lost.
During the Red Court ball in Grave Peril, Harry has brought Michael, one of the three Knights of the Cross, to the party. A particularly annoying vampire grabs Michael's shoulder and spontaneously combusts.
Michael: Sorry, that happens sometimes.
The Discworld's vampires have varying weaknesses, except the Magpyr family, who go through conditioning to overcome those weaknesses.
When they lose that conditioning, they act like this to everything. Partially because the Disc has so many gods that almost everything is a holy symbol to someone, and partially because they've filled their castle with holy symbols as part of their resistance training.
Also because of said resistance training, they actually learned and memorizedevery single religious symbol on the Disc (which is why normal Discworld vampires don't react that way to everything).
In the 1990 novella version of F. Paul Wilson's Midnight Mass, an improvised Catholic transubstantiation is done with cheap wine (in a Coke can!). One scoffing vampire drinks the wine. Hilarity (and burnination) Ensues.
In one book of SERRAted Edge series, one character blessed Seltzer Water and sprayed it right at a Banshee Whose throat was completely burned/melted away, keeping it from screaming.
The Big Bad... thing... in Summer of Night by Dan Simmons is hurt by holy water. Its servants dismiss this as a habit picked up during its time in the Vatican, leaving open the question of whether Christianity or God really has anything to do with it.
Subverted in The Tome of Bill. Holy doesn't actually burn evil; It's all about faith. If a person believes whole-heartedly in the holiness of God and his symbols, then a cross would work just fine. But if they don't have enough faith, it won't do diddly. This effect can be applied to anything that a person has enough faith in, be it a cross or a ham sandwich; Tom imbues a first generation Optimus Prime doll...uh...collectable with this effect. Additionally, there are the very rare people called Icons, whose faith in themselves is so great that they become a Walking Wasteland to the supernatural. Icons have a variety of unspecified powers.
In the first Harry Potter book, Harry defeats Quirrel hosting Voldemort by holding his hand to his face. Quirrel's face burns off because of The Power of Love from Harry's mother.
In Buffy the Vampire Slayer and associated works, vampires are burned by crosses, holy water, Bibles and other holy objects, which also fill them with irrational fear.
Used for a joke on Scrubs when Dr. Cox wants Jordan to promise him something.
Dr. Cox: I'd make you swear on The Bible, but I know how contact with holy stuff makes your skin sizzle.
Parodied on Will & Grace, when Will expresses surprise that Karen Walker can wear a nun's habit without her skin burning
Holy water will burn demons in Supernatural. Bobby apparently sanctifies all the drinks he offers people in order to weed out those who are possessed.
Forever Knight vampires are vulnerable to holy objects from any faith, not just crosses and Christian articles. LaCroix's daughter Divia is affected by the Egyptian sun disk in one episode. Nick has a bit of a tolerance to holy items, but it was still interesting when he had to testify in court and put his hand on a Bible. The cross burned into his palm.
Being Human seems to use this with the proviso that you must have faith in the symbols being used. George and the chaplain drive off a pack of vampires; the former using his Star of David and the latter quoting scripture from the Bible.
In the Doctor Who story "The Curse of Fenric", Haemovores can be repelled by faith itself. The Doctor repels them by repeating the names of all his companions, the fervently Communist Sorin repels them with a red star badge from his uniform, and Reverend Wainwright sadly fails to repel one using a cross, as the horrors of World War II destroyed his faith.
In Bram Stoker's Dracula, getting a Super Jackpot will show one of Dracula's brides being reduced to dust from a cross.
Would you believe that Vince McMahon has begun to transcend mere Corrupt Corporate Executive-dom to become a supernatural evil? WWE certainly implied such in a vignette where Vince and his son Shane are using a church as a backdrop to mock Shawn Michaels' faith; Vince imitates Triple H's water-spitting entrance using the holy water, then rubs his throat and comments, "That kind of burns a little!"
Sarah Silverman has a joke about religious harmony where she says that her Catholic boyfriend doesn't care that she's Jewish; in fact, he gave her his St. Christopher medal. "He says if it doesn't burn through my skin it will protect me."
In the Warhammer 40,000 universe, the Inquisitors of Ordo Malleus (aka. the daemon hunters) use a variety of holy objects to harm daemons, including the Incinerator, which uses this trope in the most literal sense: It's a flamethrower that fires Holy Promethium (Imperial equivalent of blessed napalm)! Not only it will reduce daemons into puddles of goop, but it's just as effective against more mundane enemies.
In Dungeons & Dragons, most evil undead and some evil other planar creatures are harmed by holy water.
Further, evil undead aren't so much destroyed by holy areas as they are weakened by it, certain divine spell caster classes may even consecrate or hallow areas at a cost, putting them at a distinct advantage against undead. Certain undead are, however, harmed more deeply by spells that simulate sunlight, and in real sunlight, such undead, specifically vampires, are destroyed quite quickly.
The Turn Undead mechanic in several versions, which is basically raw divine energy being channeled by the cleric. Depending on the power of the cleric and the undead being turned, the cleric might have just wasted a turn, might cause the undead to flee in panic or cower, or might just cause the undead to collapse in a pile of dust. (For evil clerics of evil gods, this is usually used to bolster or control the undead instead.)
Demon The Fallen had another variant — demons could not set foot on holy ground without taking damage (unless their Torment was low enough to be considered "benevolent" spirits).
In Vampire: The Masquerade, True Faith can empower its possessors against Vampires. Under V20's default rules for it, you only need one dot of True Faith to ward off vampires with an appropriate holy symbol, or deal aggravated damage with its touch — but the degree of pure devotion to your beliefs that even one dot of True Faith represents is rare.
Exalted codifies this with the 'Holy' and 'Creature of Darkness' mechanics. Put simply, anything that is such a threat to Creation that the Unconquered Sun hates it, it gets put on a list. Some powers (designated 'holy') then have additional effects when used against those on the list. These are political designations, though... some things are condemned simply because their energy signatures are close to truly evil things without being evil themselves, and there are no moral strictures about whom one can wield Holy power against, nor how.
Becomes almost hilarious when you get to the Solar charms that allow you to put specific things on the list yourself. Conjures up images of a Solar with a sharpie waiting for the Unconquered Sun to go on a bathroom break to scribble on someone's name.
In the Castlevania series as whole, this is taken literally — the Holy Water subweapon usually involves fiery burning of evil monsters.
In Castlevania: Symphony of the Night, it technically runs both ways — notable as your player character is a Dhampyr. But, there are exactly two Holy-elemental types of enemy: angelic archers in the Chapel, and the boss Richter. So the inverted version is basically useless.
Heroes of Might and Magic IV has Holy Water as an item. It can be used either to buff the hero drinking it with the spells "Bless" and "Death Ward" or to injure The Undead. Humorously, an Undead Hero can drink it and get the bonuses with no ill effects.
Holy Water has been a standard item throughout the Devil May Cry series... blasts all Mooks nearby when used, and takes a good chunk out of any boss's health-meter. Handy on the lower difficulty-levels, a vital resource on the higher ones. Many of the games have had 'No Holy Water Run' as a Self-Imposed Challenge.
In many Roguelikes, holy water hurts demons and the undead, and blessed/holy weapons do extra damage against them.
In World of Warcraft, you can find holy water in crates inside Startholme instance. It hurts the undead. In addition, paladins have the exorcism spell that only deals damage to demons and undead (in patch 3.1, it will do damage to other enemies too, but always critically hits when used against demons and undead).
In Chrono Trigger, Magus's defensive powers are negated by the Masamune, and later on in the Northern Ruins if he is in your party when making amends with Cyrus's ghost, he recoils behind his cape at the flashes of light given off by Masa and Mune.
However, it is eventually revealed the Masamune's power is anything but holy. It was forged by forcing a Dreamstone knife into the Mammon Machine, which draws its power from Lavos. Chrono's power is the closest thing to holy, and it has no particular strength against any villain.
The Elder Scrolls II: Daggerfall let you set your character to take damage from sunlight or holy places. You could also acquire these aversions by becoming a vampire. Morrowind and Oblivion continued the vampire aversion to sunlight, but dropped the aversion to holy places.
In The Legend of Zelda, this is where the Master Sword draws its true power. It started out as a divine sword in the first place, and then got further purified by several holy fires. Evil cannot survive its touch; there's a reason it's also called "The Blade of Evil's Bane". Light arrows are also this. In fact, these two weapons are the only weapons in the setting that can do any real harm to Ganon.
Of course, outside of the Master Sword, one would simply need a SilverArrow.
The Four Sword also has the "power to repel evil", but it has never been shown to destroy a great evil such as Ganon or Vaati, only to imprison them.
In the Thief series, holy water-doused arrows are by far the most effective weapon against the undead (explosives work alright too, as do, for some reason, flashbombs). Too bad holy water is extremely rare.
Averted in the Reincarnation series: the protagonist is a minor demon sent to reclaim escaped souls, who can go in a church but doesn't like it. Then again, he was after a child killer and possibly Pedophile Priest , so perhaps it was a case of being overshadowed.
In Disgaea, Flonne's protective amulet that she needs to wear while in the Netherworld (lest its overpowering evil harm her) burns the hands of any evil being who touches it. This actually provides some significant foreshadowing: The demon Vyers/Mid-Boss is not burned when he touches it, but the archangel Vulcanus is.
The storyline from Casey and Andy where Satan squares off against the Enemy Mime... and he's packing a squirt-gun. As it turns out, it was filled with holy water blessed by a dying pope on Easter Sunday directly over the holy sarcophagus of St. Peter.
Sluggy Freelance: Holy symbols also harm/repel vampires and suchlike. We usually see Riff (he being Jewish) using a Star of David on vampires, but he also put a screen on one of his robots that shuffles through the major holy symbol of every religion in case K'Z'K had a vulnerability for one of them. (When we were shown this one in action, it stopped on Ricky Martin.)
Peter Griffin: [as two New Yorkers begin to feud at church] Fellas, this is God's house...and the Patriots kick off in about 45 minutes, so can we move this along? New Yorker: Patriots suck! Peter Griffin: [gasps] Blasphemy! [splashes Holy Water in the guy's face, creating a sizzling sound] New Yorker: Ahh! Ahh! It burns! Ah, Jeez! [cutaway to a scientist in his laboratory, opening a package] Scientist: Holy water? Where's that acid I ordered?
A later Cutaway Gag features an episode of Bewitched where Darrin has enough of Endora's bull and starts tossing holy water in her face.
Homer once takes a baptism for his kids to keep them from becoming Flanderses. It doesn't seem to do any lasting damage, but the sound effect and Homer's demonic growl fit pretty well.
Subverted in a "Treehouse of Horror" short in which Marge and her sisters are witches. They show up at the Flanders home and Ned brandishes a cross to ward them off, but one sister mutters "Oh, please!" and shoves him aside. Not quite a Cross-Melting Aura because the item doesn't get destroyed. It just plain doesn't work.