Jalan.net is, by far, my favorite place to book hotels. The site has a lot of great deals and has very detailed information on the hotels: closest train station, amenities, services, photographs, maps, and what meals are included. Plus, you can search by what kind of accommodations you want: ryokan, business hotel, single, double, Japanese-style room, and so on. Until recently, Jalan was Japanese-only, but they have opened an English version of the website.
The English site features all the details of the Japanese one, and the interface is the mostly the same but has the international traveler’s’ needs in mind.