<p>I'd like to upload (via ftp) a website when doing a release build in visual studio 2008.  I don't want any source code files to be uploaded and it would be nice to configure which folders should get uploaded.  I'm using either ASP.NET Web Applications or MVC.  How do I configure VS.NET to automatically upload (and overwrite) the last deployed website?</p>

You can use the
Visual Studio Web Deployment Project
Add In from Microsoft.
I use this with MSBuild as part of CruiseControl, its very nice, and with some of the
Community Tasks for MS Build
you can do *.config (or any XML file) substitutions as part of your build process.
Edit: I also see that the MSBuild Community Tasks includes an FtpUpload action.  This should be exactly what you need.