When creating a Web setup project from within VS.NET 2003, you may notice on running the built installer that the virtual directory suggested to the user is the same as that of your project.
To change this, right click on the setup project, choose View, Filesystem, then right click on Web Application Folder and choose Properties Window. The VirtualDirectory property here is the one that needs changing.
It took me half an hour to find, so I thought I'd mention it.