Travel by Japan Rail Pass. The Japan Rail Pass is honored by the six companies that make up the Japan Railways Group and is the best way to cover ground in Japan on the cheap. A pass gives you access to the entire national railway system for seven,14 or 21 days. You can travel from Kyushu to Hokkaido simply by showing your valid pass. Restrictions apply on certain Shinkansen trains, but at these prices who's complaining?
Take an overnight ferry. This relaxing and leisurely way to see Japan has been threatened by the recent fare reduction on Japan's inter-prefecture highway system. It is now cheaper to drive a lot of places, so ferry companies are scrambling for customers. Inland Sea ferries offer incredible bargains and unforgettable scenery. Sitting in traffic jams just does not compare.
Check out the outdoors scene. Japanese are avid nature lovers, and the country features some of the best hiking opportunities in the world, from hiking in the Japan Alps to temple pilgrimages. Japanese on tour are much more open to meeting strangers than they are in their home or company settings, and hiking is an excellent way to meet people and find opportunities that might otherwise never be open to you. Ski resorts have also become very attractive, luring overseas visitors with competitive package prices.
Look for opportunities to teach as part of your vacation. If you have any experience in teaching people to do anything, put together two or three simple lessons in your native language that offer the ability to repeat and apply one or two memorable phrases, and will take one or two hours. You can earn a little money, make some new friends and get guidance to places and bargains you would never know about otherwise.
Develop a taste for Japanese food. Start now. You are going to another country, so start trying what 100 million people eat every day and thrive. You'll be surprised by how fast you pick it up. Then you'll find no need to go to a sit-down restaurant for every meal when you can live very well out of convenience stores.
