State Of The Map 2012/Transport
If you're flying from Europe, Alitalia has a good deal on flying to Tokyo. Take a look on Kayak.com. You can get a roundtrip ticket from as low as € 300. What's the catch? The flight will go from Amsterdam - Tokyo - Budapest. And you need to book it on alitalia.de (to to "Weitere Suche" and then "Multi Strecken". From Budapest airport there are several low-cost airlines to various European cities. (Still worked on July 1st)
From Narita Airport to Tokyo
A new discount bus service seems to be available connecting Narita Airport with the center of Tokyo. Until early September a special campaign will be available: http://www.japantimes.co.jp/print/nb20120630a8.html
Get around Tokyo
The best way as a visitor to get around Tokyo is by train and subway.
Tokyo has one of the most extensive mass transit systems in the world. It is clean, safe and efficient - and confusing. The confusion arises from the fact that several distinct railway systems operate within Tokyo - the JR East network, the two subway networks, and various private lines - and different route maps show different systems. Avoid rush hours if possible; trains get overcrowded very easily. (Read more on Wikitravel)
Be aware that train operation time is not 24 hours!!! Most train lines in Tokyo run from around 5:00AM to 1:00AM. When you miss the last train you may have no other choice than taking a taxi. Taxis are very pricey, but may be a value for groups of three or more.
If you are not speaking japanese fluently, make sure to carry your destination addresses as a mark on a map for your taxi driver. You might also want to give the phone number of your destination to the driver if he uses a navigation software.
Travel in Japan
The railways network makes travelling in Japan easy and fast (as long as you travel along the Shinkansen bullet train routes). There are various discount tickets for tourists (require a tourist visa), some of them need to be bought outside Japan (ie. Japan Railpass).
Highway (night) buses are generally cheaper than Shinkansen bullet trains and can save you a night at a hotel.