Loras College in Dubuque, Iowa, uses its campus
intranet to deliver timely and relevant information about college
organizations, activities, and news to faculty, staff and students.
Loras needed a content management solution that encouraged and ensured
relevant intranet updates from multiple content contributors across the
campus. By implementing Ektron CMS200, Loras reinvigorated its intranet
and turned it into a vital and integral part of the campus experience.

While the above passage is a "commercial" for Ektron, the Loras College site does appear to have a clean structure with a clear deliniation of organizations. I believe we can learn from their example.