When you buy a car, before you can actually receive it you must have a police-approved parking space within 2km of your house. That is, unless you live in a tiny village with low population density, in which case the process is much simpler (though I can't offer advice as of yet).
You can pay your car dealer to do all of this for you, although I was quoted 30,000yen which seemed like too much. To do it yourself, follow these steps:
(UPDATE 9/2013: Details about the specific forms used in this process can be found here.)
1. Find a parking space (durrr). You may need to pay for this if it is not part of your property. Fees can range from 2,000 to 100,000 yen per month per month depending on your location.
2. Obtain written permission to use that space. You will need to go to whoever owns the land - Board of Education, landlord, community centre, etc, and have them hanko the permission slip given to you by the car company. This hankoed form will be your 保管場所証明 (hokan basho shōmei): "Evidence of a place to store a car."
If you're very lucky, your employer will complete the following steps on your behalf and a week later present you with the final certificate: 車庫証明 (shako shōmei): "Parking Certification".
If not, you'll have to do it yourself...
3. Draw a vaguely-to-scale (though do measure it and include measurements) map of your parking space and the immediate surroundings (including the width of the road leading up to it). Your car dealer should provide a form for you to use for this. It doesn't need to be too accurate, but it does need to be clear.
Attach that (paperclip not staple) along with a google maps image of the parking spot in relation to your house/apartment to your hokan basho shōmei. There is a box for you to draw the map to your house, but printing one is much easier and clearer. If you print, be sure to write 別紙 ("See separate page") in the box.
4. Take all those forms to the police station, making sure you have stamped where necessary and written your name and address in all the right places (the car dealer may well do this for you). You will need to pay around 2,000yen but you can't do so in cash. Like when you get your visa renewed, you must change your money into stamps for some reason, and then affix those to your application. You do this at the police station. The station in my town closes to applications at 5:30, while the stamp window closes at 5. Applications received after 3:30 will take an extra day to process.
5. Wait. It will take approximately 3-5 working days to get your parking certification. It will come with two stickers detailing your right to park.
6. Post your parking certificate (with the stickers) and your inkan certificate to the car dealer, and your part of the deal is complete.
After the dealer receives your paper, he/she will take the car to be registered in your prefecture. With your registration details he will create a document called 車検証 (shaken-shō), which is necessary to sign up for optional insurance. He will then fax you a copy or just bring the original and a copy when he delivers the car.
One more thing - it is okay to have more than one parking space which you regularly use. For example, many Japanese teaching staff have a second, subsidised home if they have to commute. They do not need to register that second parking space.