Revolutionary Girl Utena particularly embodies the "growing up as a struggle" metaphor, with the added bonus of Gnostic metaphor thrown in for good measure. This was emphasized way more in the anime than in the manga, however.
The Show Within a ShowMagical Girl Biblion is a parody of this, complete with in-universe Rule 34doujinshi that typically follows these character types. Since Chisamecosplays the characters featured there, her Pactio Card turned her into one with a cyberspace theme.
Invoked in Mao-chan, where aliens Earth is being invaded by aliens so cute that fighting them is viewed as bullying, forcing the heads of Japan's defense forces to have their cute granddaughters fight the aliens.
Kill la Kill is the team behind Tengen Toppa Gurren Lagann's take on the genre. It borrows a bit from Cutey Honey, including the fanservicey outfit and having the death of the main character's father as a starting point for their mission. Interestingly enough, one of the original Cutey Honey mangas was written by Ken Ishikawa whose works Kill La Kill writer Kazuki Nakajima is a fan of (Ishikawa's Getter Robo influenced Gurren Lagann which Nakajima wrote when he was still with Studio Gainax) .
Princess: The Hopeful, a New World of Darkness fan supplement, adds magical girls to the mix. No Princess is going to last too long without being able to survive a fight, but the Calling of Champion has an extra dose as their purpose is to literally fight evil. In fact, the trope is an explicit part of their inspiration. There is also extra emphasis of this style in the Courts of Swords (as heroic larger than life figures), Storms (as an ax crazy version), and arguably Hearts (emphasis on noble traditions, which includes warrior traditions).
El Goonish Shive: In the later comics Elliot gains a super-heroine spell after already having the ability to shapeshift into virtually any conceivable female human form including transformation of clothes.
Last Res0rt includes a faction known as the Galaxy Girl Scouts, which seem to be a cross between Sailor Moon and the Green Lantern Corps (i.e. alien girls in whatever the alien version of "schoolgirl" happens to be).
Princess Chroma: A parody of the genre in which the magical girl is most definitely the hands-on type. She prefers fighting giant monsters with a mace over resorting to spells despite magic being the more effective, easy way to end a fight.
Fey of the Whateley Universe. Down to the backstory, the ancient Faerie who rides along in her head, her ability to summon armor magically, and a magical battle in Boston in which she and The Necromancer spent most of the fight trying to intimidate each other by calling their attacks.