The new version of the Google Apps administrator's control panel allows users to be organised into multiple domains and divisions.
This will allow the owner of multiple domains to use each as a separate entity but allowing users to share calendars or documents in any part of the organisation. There are some restrictions.
Education edition GApps administrators will be able to define their organisational structure and divide users into divisions, determining which services are available to users in each division.
Since schools consists of obviously different groups (students, staff, parents, alumni, etc), it may be useful to have domains with names that make more sense; also, defining structures for divisions will again enable services to be switched on or off.
We are about to implement some of this and will write about what happens...