Besides the excellent advice that Richard gave, a good rule of thumb is that when JR and a private line serve the same locations, the private lines will almost always be less expensive.

Contact your closest JNTO and ask for a copy of their English language RAILWAY TIMETABLE. While the ones you get from the offices outside Japan will probably be out of date, schedules don't change all that much. You can pick one up at the JNTO counter or JR office at Narita. It's a 40 page paper pamphlet, measuring 10" x 7".

There are two great Tokyo area railroad maps in English, and you can find them in the airport or Tokyo Station bookstores. The large Shobunsha Publications RAIL MAP OF TOKYO AREA is also sold at the Kisok on the Keisei Terminal 1 platform at the airport. My favorite is the smaller, easier to handle, and less expensive RAILWAYS OF THE TOKYO METROPOLITAN DISTRICT map. It's Japanese on one side, and English on the other.

One thing about the Hyperdia site is that, while it is excellent, it also produces some silly results, so I'd skip anything after the first three or maybe four suggestions.

While I read Japanese, and have no trouble using the big thick Japanese language timetables, it is only when I have to go somewhere way off the beaten path that I need anything but the English language RAILWAY TIMETABLE book, which lists all the Shinkansen and Limited Express trains, and the maps of the Tokyo area.

It's not all that difficult finding free English subway maps, as well as English rail maps for all the larger cities, such as Kyoto and Osaka.

To make it easier, Tokyo subways just went to a letter and number combination, which identifies each station on each route, and which stations you can use to transfer at. The biggest improvement is the introduction of the stored value Passnet card, which is good on 21 different private railways and subways in the Tokyo area. It's not good on JR. However, the JR Suica card is planned on being a complete (JR & private) rail fare solution in the next few years.