It is impossible to discuss Japan without discussing its geology: 10% of the world's active volcanos are here and earthquakes are a daily occurance somewhere in Japan. Japan may well be the most geologically active inhabited region on the planet. Unfortunately, while there are many resources available in Japanese on the topic, very few have been published in English.

Resources

Geology

Geological Survey of Japan The Japanese governmental agency concerned with earth sciences. Be sure to check out the Geological Museum (look under "A la carte"). (English and Japanese)

Additional