The Japanese Metro System
For inner city commuting, the metro is probably the most efficient (except maybe the heli, but that might be a bit overdramatic). No waiting for traffic, no rain and short waiting times. Depending on what city you’re in, the metro system can seem quite mind-boggling. But don’t be fooled, once you know how it works, it’s really very easy to navigate. 
image courtesy of bento.com
Navigation in the Japanese Metro
First, buy a ticket at the ticket machines close to the metro entrance. There's a big map above the ticket machines (also in English if you're lucky), with all possible destinations with numbers next to them. These correspond to the fare for the respective destinations. Select this fare on the screen and throw some cash into the machine. Out comes a tiny ticket that you can insert in the ticket gate and comes out so you can insert it again at your destination.
When you transfer metro lines of the same company during your trip, you don't need to show your ticket.
Where Should I Transfer?
There are numerous applications (for instance Navitime) for iPhones and Androids that will help you navigate the Japanese train and metro system. Just fill in your departure and arrival station, the time you want to leave or arrive and the software does the rest!