Microsoft evangelist Neil Hutson has a detailed post describing what happens when you upgrade to Windows Server 2008. As with Vista, the new upgrade procedure is actually a clean install into which your old stuff gets copied afterwards:
Instead of just installing new versions of binaries over those of an existing computer, the new operating system is installed side-by-side with the older operating system. Then the data and settings are migrated from the older version to the newer version, and then the source is deleted. While this is architecturally more correct and certainly build a clean OS install, this does cause some obvious complications that you should be aware of. Secondly in Windows Server 2008 the upgrade process is destructive to the pre-existing operating system state.
My instant reaction: there’s enough that go wrong, that a true clean install looks a great deal more attractive.