On the internet:

The Japan National Tourist Organisation (JNTO) has a new zappy web page for maps of the whole of Japan. You can whizz around the whole country and get basic maps of most areas. The maps of rural areas show road numbers, which could be useful, but the maps themselves are not zoomable in scale. The maps of cities are convenient but basic, and show train stations, post offices and major places of interest. Good for viewing on screen and getting a general idea, but they don't print out particularly well.

Again from JNTO (an older webpage), these maps come as PDFs, and display and print out more prettily, in the style of the printed maps which JNTO publishes.

Don't bother with Multimap unless you want the most basic view: it's pretty featureless when you get in close.

Google maps (link on left) give nice detail but it's in Japanese!

Joho maps (link on left) have a nice map of the Tokyo underground.

For maps of the northern island of Hokkaido, try Northern Road Navi , produced by the road authorities in Hokkaido.

Printed maps in English:

Basic maps of Japan, Tokyo and Kyoto/Nara are available free from the Japan National Tourist Organisation (see link on left).

Folded sheet maps of Japan by Globetrotter (ISBN: 1843309912), or Cartographia, both from Amazon

A useful "Japan Bilingual Map" has recently been published in paperback by Kodansha Europe (ISBN: 4770030274). Their Tokyo one is good too, mainly because of the street index, which is very handy.

Tokyo Street Map (folded sheet map) by Geocenter UK.

Indexed road map of Japan: a weighty and comprehensive monster from Kummerly & Frey.

Road Atlas Japan by Shobunsha - recommended

Shobunsha also publish a good Tokyo & Metropolitan Atlas.