Use single-site install and map entities to subdomains

I hope you are still interested in this question. I did a sub domain mapping to a custom post type using custom .htaccess setting.

RewriteCond %{HTTP_HOST} !^www\.
RewriteCond %{HTTP_HOST} ^(.+)\.domain-name\.com$
RewriteRule ^$ /index.php?store=%1 [L]

Using this setting, each sub domain will map to the store custom post type. http://apple.domain-name.com will be equal to http://domain-name.com?store=apple or http://domain-name.com/store/apple/ if you are using the pretty permalink.

Note that you will need to modify the pager if you want to map the sub domain to category or custom taxonomy.