"Magic Girls, no matter how frilly their dresses, high their screams, or incompetent their sidekicks, will be treated as the credible and dire threats they are, and I will direct as many, if not more resources to their destruction as I would for a more classical Hero."
Magical Girl Lyrical Nanoha is somewhat unusual in that rather than young girls, older teenagers and young men are the target audience, plus that it is much more character-driven compared to most other series.
The manga eventually dropped "Magical Girl" from the title, since Nanoha is now 25 and either still a Captain of an Interdimensional Air Force or higher. She's still Magical, but is a woman, not a girl.
At the same time, a Spin-Off manga starring Vivio was released that kept the "Magical Girl" part of the title. Yup, Nanoha's daughter has now officially inherited her mother's role as Magical Girl, complete with Older Alter Ego.
Mei No Naisho is an unusual example - although it's considered a magical girl series, the manga is the story of a young boy who was raised as a girl by his witch mother, and possesses witch powers, a wand and a talking cat familiar. It also features a perverted girl, as opposed to the usual perverted boy.
The Nasuverse love to play around with this. Arcueid has like 3 different magical girl alter-egos, Caren has one, and both Hisui and Kohaku have one. All are jokes. Saber Lily could be considered to be one as well, but Saber's powers are already kinda magical girlish to be with.
Magical Girl Hunters — So many girls are empowered as magical girls that they're starting to run out of sensible themes and names, and many magical girl groups are starting to target lesser evils like corporate greed. The protagonists are the eponymous hunters, hired assassins who eliminate magical girls who have become pests. Some featured deconstructions include Sailor H, the Sailor Shoggoths, and the 64 (later 128) Crayola Knights.
Do Gooders — Two members of the eponymous band are magical girls. Several other magical girls appear in the series, including Sailor Becky who wields the power of the Otaku (ripping off attacks from various anime) and Sailor Exposition who holds the power of being able to put people to sleep by extremely long explanations. There are even two different flavors of Dark Magical Girl.
Girls with Guns — Follows the somewhat nonsensical adventures of Pretty Deadly and Sailor Becky from the above two series as they take on a Crap Saccharine World by virtue of superior armaments.
Angel Moxie is both a parody and an homage of the genre. It is about Junior High student Alex (a fairly standard magical girl) and her two friends (each of whom have super powers but otherwise don't have many magical girl characteristics) as they fight off Lord Yzin and his servants. It can be found here.
It is also somewhat of a subversion, as the backstory specifies that the magical girl motif was a inspired by fiction.
The Adventures Of Sailor Ranko, a webcomic version of the definitive Fuku Fic. Ranma Saotome and Akane Tendo are sent to a new school in an attempt to get them to confess their feelings for each other and discover that Ranma's female alter ego Ranko is the reincarnation of Sailor Sun, a long lost Sailor Senshi. Ranma now has a triple life, one, as male Ranma trying to avoid the troubles he left behind in Nerima, two, as female Ranko who was accidentally enrolled at the same high school by her well meaning and oblivious-to-the-truth mother, and three, her role as Sailor Sun working with the Sailor Senshi fighting for love and justice. A Dead Fic, unfortunately.
Evil Diva, a webcomic about a devil girl who can't help doing good deeds for others.
Magical Boys!, another parody of the genre - the main character is a boy who is given magical girl powers (although he retains his gender) to battle against Dark Magical Girls who want to kill retired magical girls. As the story progresses, more magical boys are revealed.
Cutey Honey is a forerunner of Magical Girl Warrior version, which blended fanservice and fun battles in one tongue-in-cheek package. Fans are divided whether she counts as a true magical girl or a superhero.
Cutey Honey Tennyo Densetsu is set in 2005, and features a version of Cutey Honey who has time travelled from the 70s to battle Panther Claw in the new millenium.
Cutey Honey Seed is set in an Alternate Universe, where a Cutey Honey Otaku finds a beautiful alien girl who, like all members of her species, develops any power necessary to protect herself and others. After watching several episodes of Cutey Honey, she develops "super powers" just like the "real" Honey's, even going so far as to shout "Honey Flash!"
Yurara No Tsuki has elements of this, as the main character is able to transform and battle evil spirits with powerful magic.
The plot of one episode of They Are My Noble Masters is started when Ren discovers that Yume has written a story starring herself as a magical girl.
The main character in Otaku no Video is able to break into the anime industry with his magical girl series, Misty May.
The same situation pops up in Love Hina, where Kaolla Su is compared to a Magical Girl because she eats a lot, talks to animals, and can change into an adult. Kentaro Sakata and one of Keitaro's highschool friends vainly struggle to convince the main characters that Kaolla was one.
The main character in Penguin Musume Heart is obsessed with Takenoko-chan, a magical catgirl who protects the "holy place" from the evil Bamboo King. There's apparently a sequel as well, Takenoko-chan R.
Angol Moa's true form in Keroro Gunsou seems to be a parody of the Magical Girl; she has the Stock Footage transformation and special-attack scenes, the costume, and a cute personality, but she's the Lord of Terror from the prophecies of Nostradamus who came to destroy the world with the "Lucifer Spear".
Dark Magician Girl in Yu-Gi-Oh! is largely based on this idea, with several of her summoning scenes looking similar to magical girl transformation sequences. Despite the name, she is not a Dark Magical Girl.
Lampshaded: the DVD extras of Ah! My Goddess have a gag dub in which a student accuses Belldandy of being a Magical Girl. Belldandy insists that she is a Goddess, not a Magical Girl, and they then debate the crucial differences.
This was likely inspired by a situation in the manga when Sayoko witnessed Belldandy's powers and accused her of being a witch. Sayoko specifically referred to Magical Girl tropes, including the Idol Singer.
Parodied in Suzumiya Haruhi; the main characters create a movie in which the protagonist is a bunny girl-waitress from the future whose attacks include shooting laser beams, rifle bullets, and micro black holes (the last two novel-only) from her eyes.
Episode 7 of [Zoku] Sayonara Zetsubou Sensei focused on Art Shifts, with the title sequence and parts of the episode devoted to Kafuka, Chiri, and Meru as the magical girl team Model Warrior Lily Cure, and Nozomu Itoshiki as the Big Bad, The Teacher Of Despair. It even closes with an On the Next continuing the plot. This is a drastic change from the usual format of the show.
The Show Within a ShowPuru Puru Pururin of the anime version of Welcome to the NHK. Only a few snippets are shown, in which we see that Pururin is accompained by a number of animated household objects, including a vacuum cleaner upon which she flies, and that her trademark is to randomly append the word "Purin" to the end of sentences.
In Kannagi, after viewing a magical girl on TV, Nagi immediately buys a toy wand and modifies it into an impurity-vanquishing spiritual weapon to compensate for her lack of power. Then she gets really into it and starts doing poses. It looks goofy on an ancient goddess, but Nagi's clearly enjoying herself.
From the same TV season, episode eight of H2O: Footprints in the Sand had an extended sequence revolving around Otoha as a magical girl. That was probably the least odd thing in that episode.
Ayumi Kinoshita, a bespectacledIll Girl from Hell Teacher Nube, learns from her teacher how to project her astral body as a physical presence, just so she can attend school with her friends. In the process, she learns to transform it into any shape she wishes... including an indestructible Magical Girl when said friends are kidnapped.
The OVA of School Days features a parody on the Magical Girl genre, with several female cast members as magical girls.
Parodied in Bleach with Charlotte Cuuhlhourne who tries very, very hard to be one of these and fails spectacularly.
Key of Key the Metal Idol becomes more of a Magical Girl as the series progresses, though this used primarily to deconstruct the trope as Key's transformations into her more human form show just how harrowing the powers of a magical girl can be in unwitting (read Naive) hands.
The Enchantress created by DC Comics in 1966, comes very close to being a proto-Magical Girl Warrior. Young woman June Moone goes with her slightly older boyfried to an alledgedly haunted castle for a party. Turns out that there are actual spooks. June stumbles into a secret chamber, where a mysterious being tells her she is The Chosen One and gives her a transformation word. June says it and gets magical powers, an appearance makeover (blonde to dark red), a miniskirted costume, and a kickin' witch hat. The Enchantress then battles a Monster of the Week and evacuates the civilians before the castle collapses. June reappears with a weak excuse and her boyfriend expresses an interest in her alter ego. There were two more stories where Enchantress fought random menaces, but the writers didn't have a good story arc beyond that, so she went into obscurity for years, including a phase as a Dark Magical Girl.
In A Hero, Dalek Sec implies that Kyubey and the Incubators have been manipulating humanity behind the scenes, and are responsible for the rise of the Magical Girl genre, in order to make it seem like a good idea to become a magical girl. If you know Puella Magi Madoka Magica, you'll know why this is very much the opposite of true. It turns you into a soulless Lich, and worse, you will eventually turn into a monster. All while your emotions are harvested by aliens to prevent the heat death of the universe.
Even Super Sentai has an example. Gekisou Sentai Carranger, the parody series, had the kid sister of the series' main villainess transforming into White Racer, a racing-themed magical girl, to occasionally help out the heroes. Also, she had a cat/car-based mecha. Carranger was an odd year.
Megatokyo contains several of these, though the only ones seen so far are Meimi (retired), Yuki, and possibly Miho. It's been shown by the Tokyo Police and their actions that an unlicensed Magical Girl is a serious threat.
Metacarpolis has a darker than normal take in Emiko, a former Magical Girl and Pop Idol who chucked it all, moved to America and works as a cleaning service maid. Her backstory makes her look like a Former Child Star with PTSD.
Rain is huge fan of an in-universe, magical girl manga called "Black Wings Kaminari".
In The Impossible Man Yuki Shimizu is a Magical Girl, sent by her mother who leads a mysterious village of Magical Girls and Magical Women, to work as Michael Garcia's bodyguard at his store.
The German audio drama series Bibi Blocksberg is about a 13 year old witch living in a small German town and going to school with other regular kids. The series started in 1980, long before anime shows or manga became popular in Germany.
The German book series Lilly The Witch is about a girl named Lilly who finds a magical book which turns her into a witch, as well as a Mentor Mascot in the form of a little green dragon named Hector, and who has many adventures all over the world. The books have been made into an animated series on CBBC, as well as an animated movie.