Some observations from my Cybils reading:
Clockwork/mechanical animals, birds, monsters, objects, steam-punk: The Dead Gentleman by Matthew Cody, The Peculiar by Stefan Bachmann, Above World by Jenn Reese, The Brightworking by Paul B. Thompson, Goblin Secrets by William Alexander.
Ghosts: Tilly’s Moonlight Garden by Julia Green, The Whispering House by Rebecca Wade, A Greyhound of a Girl by Roddy Doyle, 13 Hangmen by Art Corriveau, The Mapmaker and the Ghost by Sarvenaz Tash, On the Day I Died by Candace Fleming, The Ghost of Graylock by Dan Poblocki.
Time travel: Caught by Margaret Peterson Haddix, Hortenâ€™s Miraculous Mechanisms: Magic, Mystery and a Very Strange Adventure by Lissa Evans, A Mutiny in Time by James Dashner, 13 Hangmen by Art Corriveau, Time Snatchers by Richard Ungar, The Freedom Maze by Delia Sherman, The Dead Gentleman by Matthew Cody, Mira’s Diary: Lost in Paris by Marissa Moss, Beswitched by Kate Saunders, The Time-Traveling Fashionista at the Palace of Marie Antionette by Bianca Turetsky.
Portals to other worlds: My Very Unfairy Tale Life by Anna Staniszewski, The Dead Gentleman by Matthew Cody, The Peculiar by Stefan Bachmann, Storybound by Marissa Burt, Iron-Hearted Violet by Kelly Barnhill, Horten’s Incredible Illusions by Lissa Evans, The Girl Who Fell Beneath Fairyland and Led the Revels There by Catherynne M. Valente, Winterling by Sarah Prineas, Summer and Bird by Katherine Catmull.
Fairy tale re-tellings: Snow in Summer by Jane Yolen, Whatever After: The Fairest of Them All by Sarah Mylnowski, Twice Upon a Time: Beauty and the Beast by Wendy Mass, In a Glass Grimmly by Adam Gidwitz, Iron-Hearted Violet by Kelly Barnhill, The Cup and the Crown by Diane Stanley, My Very Unfairy Tale Life by Anna Staniszewski, Twice Upon a Time by James Riley, The Sinister Sweetness of Splendid Academy by Nikki Loftin, Seeing Cinderella by Jenny Lundquist, The Hero’s Guide to Saving Your Kingdom by Christopher Healy, The Hop by Sharelle Moranville, The Book of Wonders by Jasmine Richards.
Orphans and street urchins: Orphans are always in season. The Dead Gentleman by Matthew Cody, Time Snatchers by Richard Ungar, Splendors and Glooms by Laura Amy Schlitz, Goblin Secrets by William Alexander, The False Prince by Jennifer A. Nielsen, Storybound by Marissa Burt, Winterling by Sarah Prineas, The Spy Princess by Sherwood Smith, The Book of Wonders by Jasmine Richards, Earwig and the Witch by Diana Wynne Jones, The Rock of Ivanore by Laurissa White Reyes, Sword Mountain by Nancy Yi Fan, Deadweather and Sunrise by Geoff Rodkey,, The Voyage of Lucy P. Simmons by Babara Mariconda, The Fire Chronicle by John Stephens, Circus Galacticus by Deva Fagan.
Talking animals and talking animal worlds: Neversink by Barry Wolverton (Arctic birds), The Secret of the Ginger Mice by Frances Watts (mice), The Hop by Sharelle Moranville (toads), Wings of Fire: The Dragonet Prophecy by Tui Sutherland (dragons), The Last Dragonslayer by Jasper Fforde (dragon), The Prince Who Fell from the Sky by John Claude Bemis (bears, wolves, and others), Sword Mountain by Nancy Yi Fan (birds of prey), Mr. and Mrs. Bunny: Detectives Extraordinaire! by Mrs. Bunny and Polly Horvath (rabbits and others), Darkbeast by Morgan Keyes (ravens, rats, and snakes), Signed by Zelda by Kate Feiffer (pigeons), Malcolm at Midnight by W.H. Beck (rats), The High-Skies Adventures of Blue Jay the Pirate by Scott Nash (birds).
Space Travel: The Prince Who Fell from the Sky by John Claude Bemis sort of fits into this genre, but it’s really more about a journey with talking animals through a dystopian future world. Gary Schmidt’s What Came from the Stars is more of a high fantasy combined with an encounter between good and evil than it is about exploring outer space. Circus Galacticus by Deva Fagan is the only real space travel book of the lot that I can remember.
Zombies and vampires: Maybe the zombie/vampire fad is still going strong in YA, but in Middle Grade fantasy/science fiction, I only remember a couple of books with zombies or vampires, The Dead Gentleman by Matthew Cody and Benjamin Franklinstein Meets Thomas Deadison by Matthew McElligott and Larry Tuxbury.