TheTechMatterAnswer: Japan Travel & Internet survival guide

TRAINS

Since public transportations in Japan are very efficient I recommend you use them, especially the trains: they are mainly operated by the largest railway company of Japan, the Japan Railwais (JR) and other private companies for a small portion of rails.

JR train timetables for the different routes can be found on this page:

http://www.japanrail.com/JR_timetableandfare.html

or here: http://www.hyperdia.com/

and here: http://www.jorudan.co.jp/english/

If you want request printed schedules you can go here: http://www.japanrail.com/request/index.html

For some train stations, the map is also available here: http://english.jr-central.co.jp/info/station/index.html

If you have to make many journeys by train and also for your convenience (you will have not to waste time to make tickets), you can activate a special subscription reserved for foreigners who visit Japan: The Japan Rail Pass http://www.japanrailpass.net. This is activated by paying in advance through one of the official dealers (list is available on the website of JR Pass http://www.japanrailpass.net/eng/en005.html) that will send you a coupon that you must exchange with the real pass in the appropriate offices (inside the train station near the international airports for example) when you arrive in Japan.

The JR pass allows you to use almost all JR trains in Japan for a specified number of days (including the Shinkansen high speed trains except Nozomi lines that make fewer stops than others).
If you have to visit Tokyo, the pass may be used freely for the Yamanote line that forms a circle inside the city, stopping in key districts.

Then there are short pieces of train lines such
Tokyo Yurikamome line connecting the mainland to the artificial island of Odaiba http://yurikamome.co.jp/english/index.php
the line connecting the center of Tokyo Narita Airport http://www.keisei.co.jp/keisei/tetudou/keisei_us/html/e_ueno.html
that must be paid for separately.

SUBWAYS

In major cities (Tokyo, Osaka, Nagoya, etc. ..) there are subway lines for which tickets must be purchased separately.
These are the subways sites of major cities:

http://www.tokyometro.jp/global/en/index.html

http://www.kotsu.city.osaka.jp/foreign/english/

http://www.kotsu.city.nagoya.jp/english/english_sub.html

http://www.city.yokohama.jp/en/sub/rosennzu.pdf

Tokyo has also a handy search engine for subways routes and prices: http://www.tokyo-subway.net/english/

In case you need a software for your phone to help you decide which subway path to take , there is a program named Metro (http://www.nanika.net/metro/) available for Symbian, Windows Mobile, PalmOS and other operating systems .

Here you find maps and information about public transportation in major cities of Japan: http://www.infomapjapan.com/access_railway.phtml

OTHERS

In other cities where there are not underground trains (for example, Kanazawa) or simply because there are few lines (such as Kyoto, for example http://www.city.kyoto.jp/koho/eng/access/transport.html ) you can use the buses, whose use is not always easy and depends on the bus type an on the city.
Buses are also available for long distances, see for example JR buses : http://www.jrbuskanto.co.jp/bus_route_e/

The taxi is recommended only for short distances (perhaps to transport the heaviest luggages), and only if you are at least 3 people sharing the ride, since it is expensive.

If you move to the other islands of the Japan archipelago (Okinawa, for example) you can use the various internal flights through JAL (Japan Airlines) and ANA (All Nippon Airlines) airline companies searching on their website all the details on timetables:

http://www.jal.co.jp/en/dom/

http://www.ana.co.jp/asw/index.jsp?type=e

In case you need to do a little day trip for brief distances you can rent bicycles (in Kyoto, for example at the north exit on the central JR station, turn left and after 100 meters you can find shop on your right).

In all cases you must always to have a small compass in pocket (is not a joke, this will allow you to better orientation in particular cases).