Jacob Morgan asks this question in his post, Collaboration in the 2.0 Enterprise. He begins with the broad Wikipedia definition of collaboration. Then points out that while collaborate may be relative simple when it involves a few people, what happens when it involves a few thousand people as in the connected 2.0 enterprise?
Since it may be hard to get everyone collaborating at once, how do you segment this into meaningful groupings? He offers some possibilities such as by geography, departments, and user created subgroups. Perhaps you might segment by feature sets or functionality, as well as. In this case certain people get wikis or microblogs.
I think the answer is all of the above. Most importantly, people in large organizations should have the opportunities to form their own groups. This approach has meet with great success at Booz Allen, for example. Rather than organize collaboration along existing organizational charts than are subject to change, they organize it around communities of interest that reflect the capabilities of the organization and the needs of the market it serves. This allows for organic growth.
Since people can join more than one group they should also be able to collaborate in the many ways they form groups within the enterprise. In some cases, this might be by geography or department. A number of the collaboration suite allows for multiple ways to look at content and connections.
I think that feature or role use should be governed by task rather than role or position. Océ takes a proper approach as they try to educate employees on when to use what enterprise 2.0 tool for what purpose. Booz Allen takes a similar approach with their change management efforts.
The challenges in implementing enterprise 2.0 are more around question such as the one Jacob raises to take proper advantage of the new capabilities the tools offer.