Ferry
Ferries are one of the nicest ways to get places in Japan. I didn't always think so; my introduction to ferries came as I shuttled back and forth between Kansai and Shikoku on small, no-frills local ferries, whose facilities left much to be desired. Then I traveled further afield and was amazed - the long-distance ferries to Kyushu and Hokkaido even have luxurious Japanese baths which you can relax in while you watch the islands move by outside the window. Some ferries even used to have discos; you can still see the glittering ball-shaped chandeliers in the large rooms at the stern...
These days, the lowest 2nd class ticket gives you a VERY narrow sleeping space (usually no smoking, thankfully - and you can request this), a blanket and a hard square pillow. A real bed in a shared stateroom might be a good investment if you really want a good night's sleep. Discount tickets are often available which makes this option almost as inexpensive as the regular 2nd class fare.
For cyclists traveling to Hokkaido, special mention should be made of the legendary Shin-Nihonkai ferry, which takes two and a half days but gets you from Maizuru (on the Japan Sea due north of Osaka), Tsuruga or Niigata all the way to Otaru on Hokkaido for the astonishing price of 9,000 yen (bicycles cost about 2,700 yen extra, even bagged ones). For comparison, the ferry on the Pacific side costs more than 20,000 yen. This ferry is absolutely mobbed in summer; reservations are an absolute must during peak times.
For other reference materials that you may find useful in route planning, see RESOURCES.
