if you would like to change the name in Application Builder, change:
C:\inetpub\wwwroot\Builder\App_Data\Sites.xml
Remember that you will have to rename to folder as well in Apps folder to be same as in Sites.xml
If you want to edit an existing application (name displayed by browser when viewing the site):
c:\inetpub\wwwroot\Apps\{myAppName}\index.html
look for <title>ArcGIS Viewer for Silverlight</title> and change to the name you would like to display
The other site settings can be done within the application builder, eg. the application title, etc.