A miko (巫女) is a shrine maiden in the Shinto religion. Given the strength of Shinto in Japan and the position shrine maidens hold in it, it is no surprise that they are a common character type in anime. Straight portrayals and dramatizations are used just as frequently as a priest or nun would be in North American or European media. If a main character, she might be endowed withmystical powers in order to fight demons, hang Ofuda so that she won't have to fight the demons in the first place, receive visions, etc. Otherwise fictional and non-fictional Miko work in shrines, often as an afterschool job. Their outfits traditionally consist of red hakama (trousers) or a long red skirt, and a white haori (kimono jacket).
Miko are more common in H-Games, because they don't have a permanent vow of chastity; they can just take over their temple when the head priest(ess) dies or quits, and then they can do whatever they want. Japanese depictions of most priestesses and other low-rung religious functionaries tend to borrow from miko, including nuns.
Another reason they are common in H-games and Fanservice-laden anime, however, is that they wear uniforms, and like many other seemingly benign and non-sexualized uniforms, the uniform itself can be a form of Fetish Fuel that is easy to get past the radar. Of course, Shinto is a little less strict about sexuality, so it isn't as sacrilegious as sexualized nuns.
Historically, a miko served as an oracle, offering prophecy in the form of a dance. In real life, most modern Miko will help out with shrine functions such as cleaning, perform ceremonial dances based on the historical versions, offer fortunes (omikuji, those little slips of paper that tell you what your luck will be like), and sell souvenirs, sometimes as a part-time job.
(Not to be confused with thatMiko. Or that one.And confusingitwithanyformofMakois just stretching it.)
Sailor Moon: Rei Hino is a miko at her shrine, which amplifies her spiritual powers. Many of her attacks are Shinto-based, and in civilian form, she can drive off monsters with ofuda. Sailor Moon's creator, Naoko Takeuchi, did miko work in a shrine as a youngster and used her experience as the basis for Rei's character, making this a case of Write What You Know.
Ranma ½: UkyoKuonji is shown as an example of the 'parttime/after-school' version in one of the late manga oneshot stories. She presumably only was there a short time or was only a 'casual' miko, as she never displayed any mystical talents during or after that story.
Arashi Kishuu in X1999. Technically, Yuzuriha Nekoi is supposed to become a miko as well, but her grandmother preferred to send her away to school and to fulfill her destiny as a Dragon of Heaven.
The Hiiragi siblings in Lucky Star, given that their father is a Shinto priest.
Miko are all over InuYasha in both major and supporting roles, particularly Kikyou, her sister Kaede (also leader of her village), and Midoriko, the "creator" of the Shikon No Tama; Kagome, although not really identified as a miko prior to people in the Sengoku era simply jumping to conclusions, also has many of the powers of a miko, apparently as a result of being Kikyou's reincarnation. There's also an evil miko, Tsubaki, who started as a normal one but was driven to evil over her jealousy against Kikyou.
Kagome's family does run what appears to be a traditional Shinto Shrine however.
In addition, Kagome was dressed as a miko at the end of the series, implying she has taken up the position now that she lives in the feudal era.
Shiho Munakata from Mai-HiME works part-time at a Shinto shrine with her grandfather, which she and her friends visit in one episode.
In the Bonus Episode of Amaenaideyo the haremettes face off against a group of mikos and a group of Catholic nuns in a game show. While they themselves are often confused for mikos in the West, they are actually Buddhist nuns.
In Rental Magica miko has a very limited set of abilities, but in this setting the main advantage of Shinto are purification rituals. Thus little Mikan almost exclusively provides cover, but she's very strong in this role and may be the most indispensable member of the team when they face something really nasty.
Riza, of Hayate the Combat Butler, is a Miko, though you wouldn't be able to tell except in the chapters where they visit her home.
The Harukanaru Toki No Naka De franchise, like Fushigi Yuugi, is centered around two schoolgirls becoming Trapped in Another World to serve as mikos to the local deity (the Yin and Yang side of the Dragon God). They are consistently called mikos, and in the manga/anime adaptations, at least one of them (Akane) has been shown wearing a typical miko outfit at some points.
Sengoku Youko has a miko in the form of Rinzu, though how much she adheres to formal duties are up for guessing, as her adopted parent is a mountain goddess.
Akeno from High School D×D is probably a (double?) subversion, she wears the uniform when she uses her strongest magic and is known as the Priestess Of Lightning (in Japanese Miko is used)... but she's also a demon.
Mahoro from episode 5 of Mahoromatic dresses as a miko while Suguru and his friends are ghosthunting at their school. Her rationale is just having some fun with the situation.
Ruka Urushibara of Steins;Gate is a subversion; he works at his family's shrine and dresses in the traditional manner, but isn't a girl at all. Double subverted when he's able to use time travel to cross into a world line where he is a girl; then triple subverted when the consequences of the timeline alterations require them to be undone.
In Dungeons & Dragons 4th edition, the third players handbook adds the Seeker class, which seems based on Miko. They are the equivalent of holy warriors of the Primal Spirits (spirit entities akin to, but separate from, the Gods and Primordials, who embody various aspects of the natural order and the real world, from blood ties to the seasons to specific creatures and placses), who seek out and destroy enemies of the natural order. They use magical powers granted by the Primal Spirits and channeled through bows and throwing weapons to create all kinds of magical effects, such as causing strangling grasses and vines to suddenly erupt from where their arrow hit the ground and ensnare all nearby enemies.
In fact, the Seeker was originally intended to be part of a "ki" power source, but the creators realized the Unfortunate Implications in producing a set of classes that shared nothing in common but the "inspired by Asia" background, and so it was broken apart. While the Seeker became a Primal Controller, the Monk, the only other apparent survivor, became a Psionic Striker.
In the setting provided in the Mecha Vs Kaiju RPG the intelligence branch of Japan's mecha defense force is made up entirely of Mikos. This makes some sense considering The original Kaiju was an Oni mutated by the Hiroshima bomb and samples of his DNA were used to create most of the others, and the leaders of the evil organization that control the Kaiju have Oni ancestry themselves
Touhou - Reimu Hakurei and Sanae Kochiya, both of whom wear somewhat non-traditional, heavily customized miko outfits; while Reimu's outfit at least keeps the traditional red and white color scheme, Sanae wears blue and white.
Not to be confused with the final boss of Ten Desires, whose name is Miko (the kanji for that name translating to "saint" rather than "shrine maiden.").
Similarly, the final class of Micaiah from Fire Emblem: Radiant Dawn is called Miko in the Japanese version (But it's read as "Shaman" as a Continuity Nod to Genealogy of Holy War.), though the only Miko-ish things about it are her usage of Light Magic and the color scheme being mostly white and red. And she loses her pantyhose.
Nanami from Valkyrie Profile. Hey, if vampires are running around in Norse mythology, why not mikos? Nanami takes a really wrong turn in the afterlife and ends up in Valhalla.
Maori from Arcana Heart. She has three miko sisters who fight with her, too.
Though not being called miko per se, the Fatal Frame series have Shrine Maidens with similar, albeit darker roles. From the first game there were the Rope Shrine Maidens chosen to be sacrificed, in a rather atrocious way, in order to prevent the Hell Gate from opening, the second had the Twin Shrine Maidens one of them was supposed to sacrifice the other to, guess what, prevent the hell gate from opening, the third had four Handmaidens, also known as Pacifiers in Europe and Japan, that wore full miko attires and performed daily shrine and housekeeping activities, as well as helping and impaling the Tattooed Priestess, another Shrine Maiden chosen because they experienced the pain of losing a loved one and had the pain of others tattooed in their skins and sacrificed to prevent the Rift, an infernal force, from spilling into the dreams of the living and finally in the fourth game there were the Kanade and the Utsuwa who performed the Rougetsu Kagura ritual to worship the lunar eclipseand summon the gate to the other world so that the souls of the deceased could pass on, of course, things go terribly wrong and the ritual fails.
The fourth game also includes the Tsukimori Shrine Maidens.
Mizuki Rashojin from the second Samurai Shodown is a rare villainous Miko, who uses her gohei as a sharp weapon and has a demonic Canine Companion to assist in the fight. However if you manage to beat her with Kyoshiro, instead of killing her it turns out that Kyoshiro had in fact exorcised her from her host Bizuki, who fell victim to Demonic Possession that took place when a purification ritual she performed didn't go as planned.
Golden Sun Dark Dawn has Princess Himi, whose default classes all have "Miko" in their names. Oh, and she has the classic red and white outfit as well.
Okamiden gives us Miko Cho, whose name should indicate that she is a Miko. Kagu also becomes one, in order to fight off King Fury.
Yuna from Final Fantasy X isn't a miko, but she has a very important place at her temple and her outfit - with its plain white top, long drapey white sleeves, large bow at the back, and long, pleated skirt - is clearly based on a miko outfit.
Mousehunt has the Sacred Shrine Mouse, a mouse with a shrine maiden outfit, talismans and gohei.
Phantom Breaker's Waka Kumon. She is armed with a "Fu-mantion Artifact" (a type of powerful spiritual weapon, in her case, a naginata) and is part of a long line of demon hunters who have been charged with taking down an entity named "Phantom."