If you're into hiking, Japan has some fantastic sites.
Not only do many major cities offer great opportunities for long walks, often off into the wilderness starting just a few hundred metres from the bustling metropolis, but there are also tons of national parks all across the country.
An excellent book on hiking in Japan, called Hiking in Japan, is well worth the investment.
If you'd rather not spend and money, however, then we have the perfect site for you:
everytrail.com is an international user-generated site much like mapmyrun or other route mapping pages. Users can create and save their own hiking routes to share with other walkers across the globe. There are hundreds, if not thousands of hikes listed, so have a look at their Japan page to find something near you.