This one specializes in children's and young adults' books but there may be some fee involved.
Internet Speculative Fiction Database: http://www.isfdb.org
Useful if you know the name of an SF/Fantasy/Horror short story and want to know what books it's in.
I'm going to give this post a BUMP from time to time to keep it toward the top of this Books board. Also, if anyone else has suggestions to add, please do so and I'll try to put them into this top post on the thread. And thanks to Bargle77 who's made some suggestions of this sort along with mine on another thread.
Also, once you've gotten an answer to your question, it's always nice to post a "Thank You" and acknowledge that you've found the answer you were looking for. And if the site allows it, it's nice to change the subject line of the thread to add on to the description something like SOLVED so folks aren't wasting time opening a thread that's already been successfully answered.
I like this one: http://www.loganberrybooks.com/stumpthebookseller/
It should be noted that this one specializes in Children's/Young Adult books.