For 9-12 year olds:
Libyrinth, by Pearl North. "Haly is a Libyrarian, one of a group of people dedicated to preserving and protecting the knowledge passed down from the Ancients and stored in the endless maze of books known as the Libyrinth. But Haly has a secret: The books speak to her. When the threat of the rival Eradicants drives her from her home, Haly learns that things are not all she thinks they are. Taken prisoner by the Eradicants, who believe the written word to be evil, she sees the world through their eyes and comes to understand that they are not the book-burning monsters that she has known her entire life. The words of a young girl hiding in an attic—written hundreds of years before Haly’s birth—will spark the interest of her captors and begin the change necessary to end the conflict between the Eradicants and Libyrarians. With the help of her loyal companion Nod, a creature of the Libyrinth, Haly must mend the rift between the two groups before their war for knowledge destroys them all."
The Undrowned Child, by Michelle Lovric. "A captivating magical fantasy in a secret watery underworld, The Undrowned Child tells how eleven year old Teodora is swept into the storybook world of invisible children whose task is to save the dying city of Venice. Working alongside the mermaids Theodora's task is immense. Together can they save the city before the water destroys it?"
Blue Moon: The Immortals, by Alyson Noel. Sequel to Evermore. "Just as Ever is learning everything she can about her new abilities as an immortal, initiated into the dark, seductive world by her beloved Damen, something terrible is happening to him. As Ever’s powers are increasing, Damen’s are fading—stricken by a mysterious illness that threatens his memory, his identity, his life. Desperate to save him, Ever travels to the mystical dimension of Summerland, uncovering not only the secrets of Damen’s past—the brutal, tortured history he hoped to keep hidden—but also an ancient text revealing the workings of time. With the approaching blue moon heralding her only window for travel, Ever is forced to decide between turning back the clock and saving her family from the accident that claimed them—or staying in the present and saving Damen, who grows weaker each day..."
Eyes Like Stars: Theatre Illuminata, Act I, by Lisa Mantchev. "Welcome to the Théâtre Illuminata, where the actors of every play ever written can be found behind the curtain. They were born to play their parts, and are bound to the Théâtre by The Book—an ancient and magical tome of scripts. Bertie is not one of them, but they are her family—and she is about to lose them all and the only home she has ever known."
The Glittering Eye, by L.J. Adlington. "Shabti wakes in a barley field with nothing but a hoe in his hand and a head full of fragmented memories. A vicious master torments his days, working in the fields with no way of escape, until a hole suspended in mid-air, leads him to a room. Two shiny gold eyes glitter back at him. Questions. Who is he? And to where does this room lead? Amy arrives in Egypt to join her archaeologist father on an excavation. All around her tombs are unearthed, opened, entered. Left to her own devices, Amy discovers a rock. But not just any rock. A great tawny cat stares back at her from its smooth surface, its shiny gold eyes glittering. Questions. Where did it come from? And what should she do now? When past, present and future collide, it's clear that some things are best left buried..."
Monster's Proof, by Richard Lewis. "Livey Ell is the only normal person in a family of geniuses. She's a cheerleader with an absentminded professor father and a math genius of a little brother, and she's sure that life couldn't get any weirder than it already is. But when her little brother, Darby, brings his childhood imaginary friend Bob to life through a mathematical proof, things start to get really strange. Bob, a creature of pure math, hates chaos and disorder in any form. And as his power grows stronger, he becomes determined to fix our disorderly world in any way possible. But that's not the only danger. People know that Bob is in our world -- including a top-secret government organization that wants to control him, and a cult of Pythagoreans who worship him."
Resurrection (Wicked), by Nancy Holder and Debbie Viguié. "The Cahors witches must come together and find Jer and Eli as both the Deveraux and the Cahors family lines face eradication. All the secrets of the Cahors will be revealed, forcing them to overcome their greatest weaknesses in order to achieve their most powerful strengths. And only united do they have any chance at victory. Before the end, sacrifices will be made, alliances forged, and old friends lost forever."
And here's one that's not fantasy or science fiction, but it sounds like it is absolutely up my alley (anyone else out there read Marion's Angels, the final book of K.M. Peyton's Pennington series? It's a book I love, and this plot summary reminds me of it).
Waterslain Angel, by Kevin Crossley-Holland. "In the village of Waterslain in Norfolk, in the 1950s, a fragment from a carved angel's wing is discovered. Maybe the wooden angels that once supported the church roof were not, after all, destroyed centuries ago, but spirited away to safety. Two children decide to find them. There are few clues, but a strange inscription on the church wall leads them into terrifying places - up to the top of the church tower, down a tunnel where they are nearly drowned. Annie dreams of the man who was sent in by Cromwell to smash up the church, and of angels flying and falling. For Sandy, whose father, an American airman, was recently killed, the angels bring comfort. The whereabouts of the angels become clear to them - but then they discover that other people are hunting for them, and are determined to stop the children at all costs. The friendship between the boy adjusting to a new life in his mother's village, and the girl whose family have always lived on their remote farm, the haunting atmosphere of the Norfolk saltmarshes, and the strong sense of the past still present, give richness to a tense and fast-paced story of detection for younger readers."