These are five websites that I access regularly, and for those living in Japan, or those interested in visiting, they all offer valuable information.
Japan Map
This is the complete geologic survey map of Japan. From the home page, click either of these
and you are taken to a map of Japan. Click on the map where you want to see, and again at the next level. The contour map is zoomable, and scrollable. Train stations, Post Offices, schools, shrines, temples, etc are all marked. A word of warning.... Japan is building new roads constantly, and in some cases the map has not been recently enough updated to include the changes, also many of the footpaths that are marked have fallen into disuse and no longer exist. I sometimes double-check with Google Maps, but it is still the map I print out and refer to on my walks, wether in countryside or city.
Hyperdia timetable
For finding routes and times for train journeys in Japan, this site is excellent. Not only that, but it is simplicity itself. Enter start point, destination, date, and time, and hey presto the first 5 choices are shown. It works with all the private rail lines as well as JR, and also includes connecting buses. Completely detailed with changes, waiting times, and ticket prices.
ZNET Japan
In-depth articles by many good historians and journalists that cover the issues you won't read about in Japan's banal and incredibly non-controversial media. Labor issues, Japan's international relations, Article 9 and military, historical revisionism, etc. much of this material is translated from Japanese. There is also a small set of links to other alternate media sites on Japan.
Encyclopedia of Shinto
This is a huge site, and is the complete translation of the Encyclopedia of Shinto into English. Laid out in the original chapters, the online version has added short videos and an excellent search function. If there is anything you want to know about Shinto, this is the place. I write a lot about shrines and ceremonies, and often this is the only place to find information in English. Any shinto terminology in my blogs that you aren't sure about, definitions can be found here.
Gensyoushi
This is a directory of thousands of the older, major, Shinto shrines in Japan. The opening page gives you a clickable map of Japan. Choose your area, and the left of the page is a list of shrines organized by old province names. Each shrine page has many photos, all the relevant historical information, and a map link.
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