Does Nausicaa count? The movie only covers a small sliver of the series, it’s one of the finest graphic novels period, regardless of hero gender.
No, though I agree that it’s probably one of the better things ever written.
Do webcomics count? I’m a big fan of Magellan, which is set in a super-hero academy, and follows the adventures of KC Jones, a young woman who’s managed to win entrance despite not having any powers.
There’s also Spinnerette, which is basically a Spider-Man parody: a student is accidentally infused with spider DNA in a lab accident, giving her two extra sets of arms and the ability to shoot webs out of her butt.
Lastly, I’ll throw out Girl Genius. Not strictly a superhero comic, it’s an epic fantasy/steampunk mashup - the creators call it “Gaslamp fantasy.” This one also exists in dead-tree format, if you want a literal hold-it-in-your-hands graphic novel.
I did read *The Time of Your Life *before I’d ever heard of Sandman, though, and I enjoyed it thoroughly - much more than *Sandman *itself. Ergo, YMMV.
Saw the OP, that was my first thought, and here it is as the first reply. Good taste that man! 
Elektra: Assassin kicked ass. Miller and Sienkiewicz both at the top of their game.
If we’re branching out into non-super genres, I’ll recommend Rat Queens by Kurtis Wiebe and Roc Upchurch. It’s a fantasy/comedy about a group of four women adventurers. It’s a recent publication (just started in 2013) and the first five issues have just been released in a collection.
Speaking of webcomics:
Gunnerkrigg Court is simply breathtaking. Here’s page 1
The heroine, Antimony Carver, is not a superhero, but I can’t tell you what she is, without giving too much away. Her best friend, Kat, might be a superhero. The Robots just call her, “Angel”. The live and go to school at the Court - a place of semi-magical technology. Annie is also called to the Gillitie Woods, a place of legendary magical and beings. The Court and the Woods are physically divided and story revolves around Annie and Kat coming to understand and bridge that divide.
There are robots. Psychopomps. Coyote. Friendly Ghosts and Insane Demons. Boyfriends that turn into birds. Homework. Minotaurs. Elder Gods. Suicide Fairies. Field Trips. Pigeons. Black Dogs of the British Isles.
The whole story is an exquisite blend of childhood, school tales, myth and magic. The art is highly stylised and just gets better as it goes along. Really, I can’t recommend it highly enough.
Definitely this. One of the craziest graphic novels ever written.
I’d recommend the first few volumes of Runaways, it’s not explicitly female-centered but there are more females than males on the team.
For shame! Even I, a casual reader know that the webs come out the base of her spine, not her anus.
Apropos of nothing, I will add that Spinnerette has the sexiest thighs I’ve ever seen.
Yet another gem from the vaults of 2000AD, Alan Moore’s wonderful Every-Girl vs. The Universe saga Halo Jones. Currently available in collected format from Rebellion, who are doing a fine job with reissues and collections.
I too came here to recommend Elektra: Assassin. Now that was a story.
Oops! I thought they came from…um…very nearby her anus. Sort of like skunks’ scent glands.
And…yeah! Sexy thighs f’sure. (Jean Grey also had sexy thighs…)
The best part of Spinnerette is the spoofing of comics standards, conventions, and clichés. Dr. Universe, as a mad Objectivist, is a delight. But, best yet, he isn’t entirely mad! He’s got some fairly good reasons for his stance. The humor is wise…and the wisdom is funny!
But, oh, those arms…
Oh, come on, having them come out from the base of her spine instead down around her anus is an obvous copout. But not as bad as Spiderman’s wrist-mounted web shooters. Still, a web comic parody … coulda gotten away with a more humorous location …
My second favorite female superhero after Empowered is Wonderella. Would make for a HILARIOUS movie, the author’s humor is topnotch.
Just read this today. Fun stuff, especially if you have an rpg background.
Might get into trouble for suggesting it but maybe Witchblade would work for you. I gave up on it but my friends still love it.
The Pro is a good satirical one.