Just so you know, The Mysterious Benedict Society is a kids' book that I read in my childhood, so I don't know how it will be to an adult reader. I think it was one of those smart kids' books though.

Just remembered another story that solidified a fear for me: the short story The Mysterious Stranger by Mark Twain. It's sort of a bleak anti-religion (or at least anti-Christian) story - there was probably dark humor in it too, since it's Mark Twain, but I read this as a child so I didn't catch it. Anyway the ending had me obsessively afraid that the world around me (and God and logic and the people I loved) might turn out to be an illusion.