According to one guest lecturer at a course about knowledge management, Åsmund Mæhle, their first attempt at creating a web portal for governmental CoP's failed because they tried to sort information in a hierarchal manner. Eg. they would put everything related to one municipality in under one node, but later failed to connect it to other municipalities having similar practices.
Their solution was to have a map-like, associative structure of information: Concepts and relations (a hierarchy typically only has one sort of relation: is-child-of).
Of course, an associative directory will be less structured, more difficult to implement and (arguebly) harder to maintain.
Certain websites require a rigid structure (legal documents, laws and rules) to guarantee no navigational mishaps or confusion.
My imminent conclusion is that larger sites, especially the portals, needs to declare certain parts of their structure an associative one, leaving a strict core with important documents in a hierarchy.