I found this post by Bob Mixon with his take on navigation for an intranet: Topical Versus Organizational.
So use both methods, a task-based approach and an organizational-based approach.
"1. Store content where it is easy for content owners to manage. If you do this, the chances of the content staying fresh is greater.
2. Create additional navigation, as needed, to facilitate the location of information from a topical approach."