I saw an MSDN Forum post today, so I looked for a ListInstance Hidden property in SharePoint 2007 features.  There is none, but interestingly enough there is one in 2010.  I wondered what would happen if you did this:

<Elements xmlns="http://schemas.microsoft.com/sharepoint/">
  <ListInstance
           FeatureId="00bfea71-de22-43b2-a848-c05709900100"
           Title="Hidden List Test"
           Description="Testing a hidden list."
           TemplateType="100"
           Hidden="TRUE"
           OnQuickLaunch="FALSE"
           Url="Lists/TestHidden" />
</Elements>

It hides the entire list from SharePoint Designer and the browser, however you can hit the list by typing in the url in internet explorer.  Pretty cool stuff.  Enjoy guys.