I have one hosting account with several, as some call them, parked domains. For example:

root-domain
sub-domain
sub-domain
sub-domain


Each sub-domain resolves to both it's own domain name, and to such variations as root-domain.com/sub-domain/ and sub-domain.root-domain.com

What are the advantages/disadvantages to allowing search engines to index my sites as both sub-domains and separate domains?