One of the shelves I keep next to the desk is my quick-reference library for all things Japanese — which is proving itself more and more useful over time, especially with the research I've been doing for the hero story and whatnot. Here's a quick rundown of some of the most immediately useful books:
Everyday Life in Traditional Japan, Charles Dunn: This is the best quick-and-dirty, all-in-one reference to the ways of life in Japan before the modern era (essentially, everything from the civil wars to about the before the Meiji years). It helps you answer quick questions, like what the months of the rice-planting season were or how many meals people date in the course of a day. The emphasis here is on factual information and not history as such, with each chapter handling a different sector of life ("The Samurai", "The Farmers", "The Merchants", etc.). This was probably one of the first books I bought for my own research on Japan and I've worn out two copies. Start your crash course here.
Japan: A Short Cultural History, G.B. Sansom: Sansom's overview of Japanese history eschews a names-and-dates approach and goes instead for looking at the evolution of Japan through its cultural expressions. It's a hugely absorbing read, one of the best ways to get a flavor for the sweep of the country's history without having to plow through a timeline.
A History of Japan [3 vols.], G.B. Sansom: If you want an even more detailed approach to Japan's history, this three-volume set from Tuttle (in paperback with a handy slipcase) is the really scrutinous version. Great for zooming in on a particular detail you might be curious about after you've already had the thirty-thousand foot view. The three volumes are also available individually.
The Cambridge Encyclopedia of Japan has proved really useful for quick lookups and other "hasty facts" work. It could really use an updating, though (it's been over 10 years since it was published).
One set I don't have, but would eventually like to pick up is the six-volume Cambridge History of Japan, which is probably the most ambitious and fully-realized work of its kind. And deadly expensive to boot, but that's what a savings account is for.
This obviously isn't an exhaustive list, but these are the books I've gotten more out of than most any other, at least so far. I'll post more lists on specific topics as time goes by.