Revenge of the Witch (geared toward readers in elementary and middle school), Foundling (teen lit), and Her Fearful Symmetry (aimed at older readers) are all books I've enjoyed a great deal and all, in one way or another, feature themes of the fantastical and horror; two of my favorites! By the way, I'd have preferred to link the titles above to the Stockton-San Joaquin County Public Library catalog but, since Sirsi Symphony seems to not support the creation of persistent URL's (at least without inordinate trouble), I'm not able to. One more reason to look at open source...
For librarians who do reader's advisory work with younger readers, both The Last Apprentice and Foundling are great choices. Neither has yet really found a large audience so the chances are that your readers may not have already read these and they are both part of larger series (The Last Apprentice and Foundling or Monster Blood Tattoo respectively). So, for readers who discover these and find that they like them, there is a lot more to follow!
Revenge of the Witch is actually something I'm reading right now (and haven't yet finished!) so I'm probably not even supposed to recommend it yet. However, I'm really enjoying it thus far so I don't feel bad about my faux pas. It's the story of a twelve-year-old boy living in a rural part of what seems to be an alternate universe version of England or Ireland. As the seventh son of a seventh son, he is selected to be the apprentice to the local "Spook" whose trade involves managing the myriad boggarts, ghasts, and witches who inhabit the region, keeping all the rest of the County residents safe from harm. Sadly, though the work of a Spook is vital, those in the profession are usually shunned by those whom they serve. The story is fast moving, really a bit scary at times, and with good character development.
Foundling is the first book in what had been previously called the Monster Blood Tattoo trilogy. Apparently, due to a failure to really take off in the U.S. in spite of its brilliance, the Australian author, D.M. Cornish, has taken the advice of his publishers who feel the series needs some "re-branding". The new cover art is much more "mature" and quite attractive, too. You'll notice that the blurb at the bottom of the cover equates Foundling with the Tolkien; it's clear from the cover art that that's a similarity the publishers want to push.
Marketing aside, I've read the entire trilogy and am at a loss as to why this series isn't more well known. Some of the best fantasy I've read in a long, long time, Cornish describes a world (the Half-Continent) of Dickensian England (with German overtones) where humans are constantly fighting to keep the world of monsters at bay. In fact, killing a monster is a high honor commemorated by tattooing oneself with the blood of your slain opponent (hence the original title of the series). This really is great stuff. The young orphan (or "foundling"), Rossamund, is entirely likeable and his closest "friend", the renowned monster killer the Brandon Rose is so memorable in her blend of fearsome appetite for the slaying of monsters, her legendary beauty, the rather disgusting biological demands that her profession makes of her, and her uncharacteristic sympathy for a poor orphan. This series is neither "only" an alternate universe fantasy-horror-adventure; Rossamund's sympathetic view of a world of monsters he feels "misunderstood" brands him as something of an outcast among his own kind while making a not always subtle statement about our propensity for demonizing our enemies.
Lastly, Her Fearful Symmetry, written by Audrey Niffenegger, was lovely. I first came across it in a bookstore (gasp!) where I judged the book by its cover (gasp!). As an aside, one of my favorite hobbies since getting an iPhone is to visit bookstores, find books I want to read, and, scanning the barcode with my phone which then links me directly to my library account, I request the titles from the library; I love it!
Anyway, that's how I first encountered Her Fearful Symmetry. It looks scary. The description sounded kind of scary. But when I read it, it wasn't scary. Sure, there is no denying that it's a ghost story. It's a story about a ghost who lives in her former London flat adjacent to Highgate Cemetary with her two, live, American nieces. Beautifully written with a cast of very engaging characters in a slow moving study of the nature of relationships (with parents, with siblings, with spouses, with lovers, with pets!) I found myself entirely loving this book even though it wasn't what it was portrayed to be. Until the final chapter or two, when this story suddenly bloomed into unexpected horror. How totally awesome! I wouldn't dare reveal the shock but I'm telling you I was shocked! Wonderful read!