Anyone can be a Tokyo public transit guru but it requires having two different publications, from different publishers:
1. The paperback "Tokyo Metropolitan Area Rail and Road Atlas," published by Kodansha. Last one I bought in the U.S. was $24.
This book contains the most complete listing of all rail and subway lines, including private rail, with a good indication which stops are express and local and also indicates travel times. All names are bilingual so you can do a pattern match if need be (generally only required when looking for stations other than the one you're at on private rail lines or buying tickets on private rail lines).
2. "Rail Map of Tokyo Area," published by Shobunsha in English and sold for Y800 in Japan. This one shows better than any other the largest number of transfer points (although it doesn't have all of them), and is particularly useful when determining the shortest route if you will need to transfer between subway, JR, and/or private rail.
It is imperative to get the latest edition of both as public transit keeps getting added to in Tokyo. Any book or map that doesn't show the Oedo subway line, for example, is out of date.
I am aware of at least two new JR rail lines passing through Shinjuku (the Shonan Shinjuku line that goes to Yokohama -- and beyond -- and the extension of the Saikyo line that connects to the Rinkai line) that are not yet on any English publication I have seen, but with these two guides and some planning time, you'll be even occasionally able to outdo a local.
The "Rail Map" is a particularly good map to pull out when someone from London or Paris or New York tries to boast about how extensive their public transit system is!
(Edited for typo)
[This message has been edited by RichardInSF (edited Jan 30, 2004).]