winterkoninkje | Travel tips (Reply)

The following links can be of great use to anyone traveling to Japan:

Japan Railways Group — The umbrella website for JR with links to the regional sub-companies.
HYPERDIA-timetable — a digital timetable and fare table for shinkansen etc. Enter your travel plans and it will tell you how to get there and, more importantly, how much it'll cost.
JR-East — for Tôkyô and northern Honshû. Their fare calculator, somewhat less useful than Hyperdia, but still nice to have on hand. Also tickets other than JR passes.
JR-West — for the Kansai region (Kyôto, Nara, Ôsaka, Kôbe). Their JR railpass page.
world eki-net — site for making reservations
Japan Rail Pass — main site for railpass info.
Jalpak — one of the places you can get an exchange order voucher for JR passes.

Hostelling International — make reservations at all manner of hostels.
International Tourism Center of Japan — many listings for affordable lodging, particularly ryokan (traditional Japanese-style inns). Requires passport number to make reservations, and larger cities are listed by subsection which makes it awkward to search unless you know them.