An interesting Project Management Information System using Sharepoint was outlined in the book 'Seamless Teamwork' by Michael Sampson, published in 2009.
His design began with a sub-site using the 'Blank' template. Within this space, 2 peer subsites based on the 'Team Site' template are created. One of these sub-sites is for the project team, and the other is for stakeholders and sponsors.
There are thus 3 separate spaces, with 3 separate sets of permissions. The entry site (a 'Blank' site) has the least restrictive permissions, permitting all who have legitimate interest in the project to view announcements, etc. that the project team and the project sponsors and stakeholders choose to make 'public'.
With more restrictive and distinct permissions are the co-equal sub-sites for the project team and for the stakeholders and sponsors. Each of these 'teams' can communicate and collaborate about issues important to them without making sensitive information available to the other team.
The sub-site used by the project managment team might very well create other sub-sites such as a Wiki site, though Sampson thought a wiki page library would work better in most circumstances. This sub-site would of course be the workhorse of the 3 sites.
This sounded like an excellent site design for Project Management. Feedback? Experience?