Although I haven’t had any problems yet with a car. I owned an old Light bodied “kei” car before, and currently earn a big hybrid car that gets about the same kilometers per gallon as the kei car did but seats eight.
A very long time ago I wrote about getting a license and some advice for people who have to take the test (like Americans do) here : “Advice for the Driving Test in Japan“.
Once you have a car (or if you plan on getting a used car) you are going to come up against two big money drains… the “shaken” car inspection, and taxes. The bigger the car, the higher both of those will be. For some in depth information on the “shaken”, check it out here at the Big in Japan blog “The Shaken: A Motoring Scourge in Japan”. Dave over at Big in Japan often writes about cars, so if you’re interested in cars in Japan, please go check it out.
If public transportation is an option for you, and your place of work will pay for it, you can save a lot of money by avoiding buying a car, but if you have a family, or live or work in an inconvenient place and have no choice, well… good luck to you!