This obviously depends on where you come from. From Europe, the best deals can be found from London or Paris. The airline itself is not very important. Some, such as Lufthansa, offer youth/student discounts. From the US, the cheapest flights are from L.A.

 

 

The Internet is a good place to start looking.

 

From Japan, check No1 Travel, Across Travel, STA travel in English or Yahoo Japan Travel in Japanese.

 

 

If you can't stand planes, it will unfortunately be very difficult for you to reach Japan. Sea Travel is long, tedious and expensive, unless from Korea, China or Russia. Coming from Europe, you could take the train across Russia, then a ship to Japan from Vladivostok or from China. However, this requires you to get a proper visa for Russia/China, and therefore apply before you leave (visas to Russia are particularily hard to get outside organised tours).

 

In central Tokyo, there are 2 main subway/underground companies : Eidan  and Toei . There are numerous other private companies deserving the suburbs (Seibu, Tobu, Tokyu, Keikyu, Keio, Keisei, Odakyu...). Japan Railway (JR) has train lines nationwide, but usually not where private companies are already present.

 

You can check train timetables (time schedules) for all Japan on Yahoo Japan Transit or Ekitan, though both sites are entirely in Japanese.

 

 

Commuter tickets are useful if you often travel between 2 determined stations, for instance, between your home and your work or school. Season tickets valid on all subway/underground lines are rather expensive and not common in Japan. Each train company has different tickets, however there should be a possibility to combine commuter tickets.
To buy one, you will have to find a station that has a commuter ticket office (usually big stations). Once you are there, you will have to fill an application with your name, age, address, telephone, and most importantly, the 2 stations between which you want to commute and the length of validity of the ticket (usually 1, 3 or 6 months). Your ticket will enable you to use any station on the same line between the 2 stations selected, but no other. If your journey involves several changes, you might be able to use different lines to reach your destination. For example, an Eidan Chikatetsu commuter ticket from Nihombashi to Shibuya should be valid in all Eidan lines and stations between these 2 (i.e. Ginza-line, Tozai-line till Kudanshita, Hanzomon-line from Kudanshita, Marunouchi-line between Otemachi and Akasaka-Mitsuke).

 

 

Teikiken = commuter ticket
Chikatetsu = Subway, Underground, Metro