I was also going to suggest Susan Cooper's Dark is Rising series. Very intriguing.
Sea of Trolls by Nancy Farmer--Viking adventure and mythology, really exciting, thoughtful, and often funny. I think it's at least a trilogy now, and the books are pretty sizable. I think the main character is about 12, so more of a Harry Potter level.
books by Walter Moers--I read "The City of Dreaming Books" and loved it. So there's these dinosaurs, that wear clothes and live in houses and love to read, and one of them going on a quest to the big city to find the author of the most awesome story in existence. And really cool, weird, delightful stuff happens. He's written several other books that look equally creative, although I don't know if they're part of a series. They're hefty, though.
Children of the Lamp by P.B. Kerr--I've read the first one, about a pair of pre-teens who learn they're actually djinn (genies). Really interesting new set of fantasy rules, I thought. Again, Harry Potter level.
Stravaganza by Mary Hoffman--In the first book, an ill teenage boy finds he can escape to an alternate universe similar to Venice. Political intrigue, magic, and some fun alt-history stuff. Also some strong female characters. There's at least four books.
If you like teen adventure fantasy, there's Ranger's Apprentice by John Flanagan, and Last Apprentice by Joseph Delaney. Both have magic, but the latter is more ghost-busting and the former more straight fantasy. That's my impression from the first books, anyway.
Wise Child by Monica Furlong--Set in ancient Scotland, a young girl is taken in by the local witch/wise woman. At least three books.
Septimus Heap by Angie Sage--Definitely for kids, but the books are fat and there are at least four of them. Reminds me a little of Discworld and Stardust. Princess raised in secrecy, missing seventh son of a seventh son, a bit goofy sometimes.
Artemis Fowl by Eoin Colfer--In the first book a 12-year-old criminal mastermind uses high technology to deal with the world of fairies. At least six books.
The Enchanted Forest Chronicles by Patricia C. Wrede--Starts with Dealing with Dragons. Fractured and up-ended fairytales, lots of strong female characters. Each of the four books is slim, so maybe look for a compilation.
His Dark Materials by Philip Pullman--Breathtaking world-building in a place that's kind of familiar, and yet not. The first book is really amazing, and the heroine is strong and complex.
The Mysterious Benedict Society by Trenton Lee Stewart--In the first book, a group of genius children are gathered together to infiltrate an evil training camp for kids. Clever and wacky and fun.
If straight historical is okay, check out some of L.M. Montgomery's books--most famous for Anne of Green Gables, but there's several others she's written as well, generally with well-defined young women in the lead. Or for historical royal intrigue, Jean Plaidy seems to have written at least one novel about every monarch of England--they do skew a bit romancey, but there's lots of history and politics going on as well, and often multiple powerful female characters.
Carolyn Meyer is also great for historical stuff--there's at least five independent books in her "Young Royals" series, focusing on young Elizabeth I or young Catherine de Medici, etc.--and she's also written books about young women in the Old West and the Trojan War. Karen Cushman is also great--I started with "Catherine, Called Birdy" about a rebellious medieval teenage girl, and she's also written a number of other books with young female protagonists in both the middle ages and the American West.
Anna of Byzantium by Tracy Barrett was great. Strong female character, almost unlikable, struggling to survive in the royal family of the Byzantine Empire. Daughter of Venice by Donna Jo Napoli was also a really good look at a young woman in a historical society I knew little about. Both of these authors have several other books, not sure if they're really series, though.
Princess Academy by Shannon Hale--A series now, I think. I read the first one and it was really good. Girls from remote parts of the (fake) country are gathered up in a school to be educated as a future bride for the prince.
Gail Carson Levine does nifty twists on fairytales with strong female protagonists, like Ella Enchanted.