I've just been around Japan and this book is an absolute must for anyone wanting to do the same via the ultra-efficient train network. I managed to get round virtually all of it with this and a basic phrasebook with very little knowledge of the language.
The main section of this book is split by area, (eg Hokkaido, North, central and west Honshu etc.) then into two sub-sections; Route guide and City Guide. The Route section deals with how to get from one major city to another via the train network and the latter deals with what you can do when you get there. Most stations, large and small are covered on each line, with suggestions about when to stop off on your journey to take in the sights. The City guide covers most major cities and provides maps showing places to eat, stay, and see, as well as other useful things such as Internet Cafes, subway stations etc. (This section was not quite as useful as it sounded as the hotels listed are often more expensive than what you can get if you just pop into the local JTB branch found in every city.) For all the local attractions, it also lists the opening times and price, and these (at the time of writing) are pretty accurate.
There are other sections as well either side of the main one: There is a detailed section on the history and culture, along with itineraries and recommendations, along with frameworks of what you might want to do depending on how long you'll be staying. There is also a guide to how to get hold of your invaluable Japan Rail Pass, which you'd have to be barmy not to use if you intend to be there for a week or more. (Tip: Don't bother with the green passes - the standard carriages are more than enough luxury compared to the trains in the UK). Finally, there is a section at the back with numbers/dates/days of week etc. translations, useful phrases, and some basic timetables that can be used as a rule of thumb when getting from place to place.
The book in general has an emphasis on the JR lines (because that's what the pass is valid for), but does have some information about connecting lines in order to get to recommended destinations along the way. It would be nicer if there was a little more information about the non-JR sections and what there is to do along them, but there is only so many pages and the text can only be made so small, and its already packed to the gills with interesting and useful info already.
Overall, thoroughly recommended. Especially now as its been updated (2007) I took many books with me and found this to be enough for almost all my needs, hence why my copy of this one is so dog-eared and the others are pretty much mint. :)