The Bone Garden and A Cursed Inheritance by Kate Ellis - intelligent, interesting mysteries with a historical twist, featuring a young black police inspector in Devon (England) named Wesley Peterson. Peterson studied archaeology in college, and in both of these books a murder that he is investigating intersects with an archaeological dig on which his friend Neil Watson is working, and the present day solution, at least in the first book, echoes the past events.
Below the Root by Zilpha Keatley Snyder (I've always loved that name) - in a "perfect" society, ominous rumblings of things gone awry and corruption at the top. I read this when I was a kid and along with some others that I liked, managed to get another copy through paperbackswap.com (a great site, if a little top heavy with romances). Although the setting is pastoral rather than underground, this reminds me a lot (or really, the other way around since this was published first) of The City of Ember. I'd never realized that it was the first of a trilogy, so if I like it as well as I remember I'll have to try and get hold of the other two. I loved her books as a kid, especially The Egypt Game, The Changeling and The Headless Cupid.
Elleander Morning by Jerry Yulsman - a fascinating thought experiment. A copy of the Time-Life History of the Second World War makes it into a parallel universe in which there never was a Second World War, and a nuclear-armed Germany decides to use it as a playbook. This is another one that I read when it first came out in the 80s and picked up again through paperbackswap.com. The personal story of the woman who finds herself hurtled backward in time and uses the opportunity to kill a young Viennese artist named Adolf Hitler, and her granddaughter in the new world she's created, attempting to find out what happened, are in the foreground, but the premise is fascinating. I haven't finished it yet, so don't know if he manages to live up to the expectations he creates.
Autism's False Prophets by Paul A. Offit - I can't recommend this book highly enough - I may even get off my duff and actually review it. An excellent review of the hold vaccines-cause-autism "school of thought" including an examination of the social and cultural forces that allow this kind of bad science, as he terms it, to go mainstream and actually be accepted by large numbers of people. For now, I can't do better than to link to an excellent review over at the ScienceBlogs Book Club.