But what you want is a JR Pass - best value if you have some longer shinkansen trips planned.
You must buy this in your country - they can not be purchased in Japan.
When you arrive you get it validated at Narita (easiest) or Tokyo Station (difficult to find the one place that allows you to do this). Other stations may allow it as well - I saw this week at Shibuya a sign for validating the pass for the first time (been here 7 years).
If it is all in and around Tokyo your best bet may be the suica or passmo - you can not use JR Pass on anything but JR, so no buses, no subways and no private rail. Suica and Passmo you canuse on most everything - enter and leave via the wickets with yellow tape on them to "transfer" and it may save you money.
There are also day tickets for JR and Subway - also weekend I think. These are great value if you are doing a lot of travel on one mode of transport - e.g. subway. But also beware as there are two subway companies!
A couple of links:
TripTouch
Jorudan
For Asia travel in Japan is quite expensive - but if you are coming from London then it is very cheap!
Another tip is that if you can not make out your station because it is all in Japanese (very rare these days) then the best thing to do is buy the cheapest fare. Then when you get to your destination go to the excess fare machine and it will tell you if you need to pay more and if so how much. Nearly all ticket and excess fare machines have a button for English instructions. There are no fines (as in the UK) for travelling beyond your ticket - everyone does it!
