There is an MSDN article here which suggests that you just move the projects to a new directory.
However, as you mentioned, the list of projects is kept in the registry under this key:
HKEY_CURRENT_USER\Software\Microsoft\VisualStudio\<version>\ProjectMRUList
and the list of recent files is kept in this key:
HKEY_CURRENT_USER\Software\Microsoft\VisualStudio\<version>\FILEMRUList
Note For Visual Studio 2015:
The location has changed. You can check out this answer for details.
Some people have automated clearing this registry key with their own tools:
Visual Studio Most Recent Files Utility
Add-in for cleaning Visual Studio 2008 MRU Projects list