If you are going to spend time in Tokyo, consider buying the GRUTT pass ^ . You can spend a week there and never have to spend more than the 2,000yen cost of getting it as it covers entrance fees to so many museums and galleries.

http://www.flyertalk.com/forum/showthread.php?t=465005 (this year's details under post number 11)

There are discount schemes available relating to many travel tickets. For instance, the Hakone Free Pass comes with a list of admission discounts for the Hakone area. I understand this is true with some of the Kansai region rail cards too.