There're a couple of ways to accomplish this, but the first thing I would look at is using the RBS structure to govern how security is propogated throughout the organization. Identify how many branches you need for the RBS, and configure Category security
appropriately.
That should get you most of the way there.
Alternately, you could use either a custom Project field or the Department field. Then create specific Project Center views, each view filtered on a different department. In this case, you would have to create a Security Category for each department,
and make sure it only possesses the correct views, and that the right users are mapped to those Categories via Security Groups.
My recommendation would be the first option as it will make administration a lot simpler. Take a look at the Project Server RBS functionality and see if it meets your needs.
