Which rental company should I use?

The service industry in Japan is such that you won't ever get really "bad" service compared to back home (wherever that may be). That being said, I have noticed a few differences in terms of rental agencies that I've used over here from time to time.

Nissan Rent-a-car

This is the company I have used the most, as they have the best hours (many with 24 hour locations), usually the best prices, as well as a good variety of cars. The services they provide are very basic and speedy, and also allow you to drop off the car free of charge if its within 50km of the original outlet. Most of the outlets are in really great locations as well, being either near major train stations or just about any airport in Japan.

I have only had one seriously bad incident with this company. I rented a car in Kyushu near the Oita ferry terminal, and they gave me an older Nissan March because it had English speaking satnav. It was nice of them to do so, but I would have rather had a newer car with the newer Japanese satnav. I took the car anyway, and on the last day of the trip we noticed a tire was really low. We got it checked at a service station, the inside of the rim was actually bent from the previous renter (we hadn't had a single misstep on our trip!). They put the spare on, and we took it back to Oita where they tried to charge us 20,000JPY for the broken tire. At this point we argued with them for about 30 minutes, and explained that it was Nissan's responsibility to check under the car, and mine was to check for cosmetic damage at the time of rental. Eventually we won the argument and they let us go free of charge.

Don't let this discourage you. If they try to rent you an old model, ask politely for a new one and check the outside of the car thoroughly.

Nippon rent-a-car

I've only used them once and I wouldn't do it again. Their prices are higher than Nissan, and they gave us a Prius with over 100,000km on the clock that was pretty beat up inside and outside by Japanese standards. The worst bit was the brakes which really felt as if they needed to be serviced or inspected.

That being said, they will rent you an ETC card for 300 yen a day which can lead to serious savings on the highway on weekends and holidays. Something to think about then.

JR Rent-a-car

I've only used JR's car rental once as part of a Shinkansen/hotel package up in Aomori Prefecture. It was really well run and they had us off the train and in the car within 15 minutes of arrival. We were also given what looked to be like a brand new Honda Fit with only 1700km on the clock. JR car rental outlets are usually located at major JR stations, so they can be really convenient if you're coming off of a Shinkansen or Limited Express train in a rural area especially.