MSI installation projects created in Visual Studio 2003 allowed the setting of a PORT value. This port value would be used to search the IIS sites and install the web application by default on the first site that corresponded to the specific port.
Users migrating from Visual Studio 2003 to Visual Studio 2005 have found that support for the PORT property has been removed and there are few technical options available to solve this problem.
This article outlines how using Visual Studio 2005 SP1 and a command line and MSI custom actions to install a web application on a site configured for a specific port.
After an update to VS 2008, I see no options that resolves this in VS 2008 either.