Two good articles on web deployment projects in ASP.NET 2.0:
http://weblogs.asp.net/scottgu/archive/2007/06/15/tip-trick-creating-packaged-asp-net-setup-programs-with-vs-2005.aspx
http://msdn.microsoft.com/msdnmag/issues/07/04/ExtremeASPNET/default.aspx