If you stay more than 90 days in Japan you are required to register with the Japanese government and carry a Residence Card (Zairyu Card).
Japan changed its system somewhat in July 2012, but the card system is essentially the same. The registration card however now has more data, including biometric data on it, and you need to register at a government office with 14 days of moving into your residence.
When you first enter Japan on a medium/long term visa, you will be given a residence card at your port of entry that you need to take to your local government office. If you change your residence you must get a certificate of moving out (Tenshutsu shomeisho) that you need to submit to your new local government office.
Noteworthy changes are that now you are listed like Japanese are, as a basic resident (juminhyo). Also changed is the re-entry system for leaving Japan and coming back. Long a thorn in the side of long-term residents, a 3000 yen charge for leaving and returning to Japan (or 6000 yen for multiple entries) was changed to a free "special re-entry permit" if returning within a year from departure (or before your current registration expires, whichever is earlier). The maximum status of residence was also raised to five years from three, but for a "College Student" the maximum period of stay is 4 years and 3 months.
You must carry your residence card with you at all times (unless you are 15 year old or under) and present it to any policeman or immigration officer who requests to see it. Failure to do so may result in a trip to jail or a stiff fine. Legal permanent residents must apply for the new residence card within 3 years from July 2012.