I'd do it differantly. Set up your DNS to point all (any)
hosts to your domain, so someone could type anything as the host
such as subsite1.mywebsite.com and subsite2.mywebsite.com. Then you
only need one application.cfm where the name of the application is
the domain name with cgi.server_name. You then define your sites in
the database based on their unique URL. This is also handy if you
need to break your busy sites accross multiple jrun instances or
servers.
You could then apply differant layout per application and
differant config, directories etc. You can look at fusebox 5, since
that framework can apply layouts based on variables.