Without me realising it Amanda Murphy's blog somehow dropped off my blogroll (possibly when she moved to feedburner) which is a shame because it means that I missed her article on the differences in the way site collections are handled between 2003 and 2007 the first time around.
Now that I needed that information however, it's good to see that my Google-Fu didn't let me down AND I got to update my blogroll so Amanda's back on my reading list again. (Note to self – check feed reader to see if any other reliable posters have "gone away" for no apparent reason).
The points she raises are interesting and there's a big architectural choice implicit in them – namely when you create your MOSS 2007 architecture, what do you actually want to place as the top-level site in the default site collection running in the web application using port 80 i.e. what will your users get when they go to http://yourmoss2007server/ ?
Amanda's right in that for a number of organisations it will need to be some kind of portal (and I see that in the RTM code we ended up with templates for both "Collaboration Portal" for a traditional sharepoint-ish portal and "Publishing Portal" for something which sits more comfortably in the old CMS space).
However this won't necessarily always be the case – the local government customer I'm currently running a pilot for has a relatively mature Oracle portal as their standard intranet organisational portal, which acts as the gateway into a number of their line of business applications. There are a number of technical (and even more political) reasons why that's not going away any time soon, so from their perspective the primary role for MOSS is for collaborative working and document management.
We've done a fair bit of work with them on understanding what their WSS teamsite hierarchy needs to be based on their own functional structures and the extremely hierarchical nature of their information corpus, driven (to a great extent) by the mandates of the government classification list.
For them, the best fit seemed to be a site collection which gives them two tiers of site classification based on a modified version of the site directory (in which no content-holding sites actually exist – as you would find in a records-management based fileplan) with the actual collaborative sites appearing at level 3 and below.
As with all information architectures it's somewhat of a compromise – it means we've ended up with a reasonably large number of "empty" sites to build the classification skeleton, but it did create for them in a relatively simple and vanilla fashion a structure whereby the collaborative sites themselves sat within an explicit context within a defined hierarchy, which was one of their key business drivers.