Ecotourism or green tourism started getting attention in Japan about 15 years ago, and if you carbon offset your airticket (which some tour agencies will now help you with) you could probably spend a rather planet-friendly week or two over in these parts of the woods.
More details over at Treehugger!
Ecotourism Japan may be the best website for planning your trip. They introduce trips to the Kiritappu region in Hokkaido, the Whole Earth Nature School at the foot of Mt. Fuji in Shizuoka Prefecture, and Picchio (Karuizawa region in Nagano Prefecture).
For the conservation and prudent use of regional resources Picchio has developed four well-balanced projects: the Preservation and Management Project, Environmental Education Project, Ecotour Project, and Research Documents Project. Especially, the research on Asiatic black bears focusing on the coexistence of bears and humans has lead to the development of high-quality programs and has had a positive impact on regional development.
Here is my brief list of things to do on a greenish summer holiday to Japan:
1) Hotsprings - enjoy the volcanic activity that heats up mineral water for your bath, naturally
2) Mountain climbing/hiking - Japan's highest mountain, Mt. Fuji, is not the only tourist spot!
3) River rafting - just two hour northwest of central Tokyo, there are great rivers like the Tone
4) Scuba diving/ snorkling - Okinawa or the Ogasawara islands with corals and rare ocean fish
5) Shrines & temples - these are the spiritual "homes" of Japan, and for many foreigners too!
So, come on, I know you have been around. What would you like to add to that list?