Hello, I am Yoshi from NILS Japanese language school.
A new residencey management system started on July 9, 2012. This new system is applied to foreign nationals residing legally in Japan for more than three months. The alien registration system was abolished wih the start of this new system.
Let me tell you two major changes with this new system.
1. Residence card:
The new residency management system issues you a resident card instead of an alien registration certificate. You always have to take the card with you as before.
2. Special re-entry permit:
You are not required to apply for a Re-entry Permit if you leave and re-enter Japan within a year of the date of your original departure.

You can see the details about the system here.

July 11th News, from NILS Japanese language school.