Microsoft has a utility called UPHClean (direct download link) which helps unload the user session quickly and completely at log-off or shutdown. I've tried it and it's significantly reduced the amount of time it takes to shutdown my PC.

The User Profile Hive Cleanup service helps to ensure user sessions are completely terminated when a user logs off. System processes and applications occasionally maintain connections to registry keys in the user profile after a user logs off. In those cases the user session is prevented from completely ending. This can result in problems when using Roaming User Profiles in a server environment or when using locked profiles as implemented through the Shared Computer Toolkit for Windows XP.

On Windows 2000 you can benefit from this service if the application event log shows event id 1000 where the message text indicates that the profile is not unloading and that the error is "Access is denied". On Windows XP and Windows Server 2003 either event ids 1517 and 1524 indicate the same profile unload problem.

To accomplish this the service monitors for logged off users that still have registry hives loaded. When that happens the service determines which application have handles opened to the hives and releases them. It logs the application name and what registry keys were left open. After this the system finishes unloading the profile.

All it does is watch for handles to your registry at shutdown that do not appear to be closing in a timely manner. It will not fix any apps, break any apps, or do anything to apps. All it does is close registry handles.