Takamitsu Sawa–a prominent policy analyst working on environmental issues in Japan–has an informative article in the Japan Times on how Japan might reduce its CO2 emissions.
His main policy recommendation is to build more light-rail lines. Tokyo–being one of the most densely-populated places on the planet–has a pretty expansive train and subway system and an expressway system that used in excess of its capacity. However, many other cities in the country are less-equipped.
Sawa argues in favor of a system that has parking on the outskirts of the smaller urban areas where people could then transfer to light-rail to reach inner-city destinations. He is less explicit about how such systems would be financed.
Kiyohito Utsunomiya wrote a short article (.pdf) a couple of years ago in the Japan Railway and Transport Review making a more detailed case for light-rail transit and he nicely compares Japan to other countries. The main obstacle facing Japan is the history of not subsidizing transit. Utsunomiya notes a few examples from the 1990s where the national government gave some assistance for capital improvements, but railways are expected to generate enough fares to meet operating expenses.
Another unique way rail systems can contribute to energy savings is documented in the Real Tech News blog. They report on efforts by East Japan Railway Company to harness the energy produced by each passenger when they push the turnstyles at stations to power the electronic systems that monitor fare cards and grant access to the stations.
This type of energy micro-production stands in stark contrast to conventional wisdom where by energy needs are provided by large-scale industrial facilities.