People wax lyrical about Tokyo transport: extensive, efficient, reliable, clean, safe and relatively easy to navigate. I concur. The longer I am here, the more I appreciate it, no doubt aided by the constant lamentations in the Sydney papers about public transport there.
It is extensive. Extensive to the point it doesn't really fit on one map. Below are the JR and subway maps, but neither includes many of the private lines that branch out from Tokyo. Aside from Japan Rail which has more than 10 lines running into central Tokyo, there are 13 subway lines - some owned by the National Govt. some by the Tokyo Metropolitan Govt, at least 4 monorails, 7 or so private rail companies with varying numbers of lines*, at least 2 trams, 2 bus systems and local govt buses that do loops from the train stations to key points like libaries and sports centres, a river boat.... have I remembered everything? There is a map that manages to integrate all system - but it only shows very central Tokyo.
The link below is the most comprehensive transport map I have seen of greater Tokyo. It's phenomenal. I can't say it's the most useful, because it's so big, but if comprehensive is what you want, it's probably the best.
In theory it sounds dificult to navigate, in practice it's easier. There is a plethora of websites and mobile phone websites where you can enter place A and place B and it will give options for how to get from one to the other. (including http://www.jorudan.co.jp/, http://www.hyperdia.com/ ) There is the flexibility to search by the cheapest, the fastest, the least walking, by excluding private lines, excluding express etc. It also can tell the time of the first and last train. Most lines stop around midnight and start again around 5, which can be an irritation. People generally know their own trainlines first and last train time as well as which stations they can change for other lines. Navigation is also made easier by colour coding. Each train line has a designated colour that is evident from the outside of the train, as well as on maps and on platform signs. Trains only travel on the one route. Signs and announcements on the train also inform, often but no always in English as well, which lines intersect with each station.