Crossdomain.xml on a multisite setup
I would make up a module with a hook_menu in it with a path of "crossdomain.xml".  In the menu callback, figure out your domain and serve up the proper file with the proper MIME type.  Install the module in "sites/all" and enable for each site that needs it.

I also suspect you could handle it in .htaccess with something like

RewriteCond %{HTTP_HOST} ^www\.host1\.com [NC]
RewriteRule crossdomain.xml crossdomain.host1.xml [L]
RewriteCond %{HTTP_HOST} ^www\.host2\.com [NC]
RewriteRule crossdomain.xml crossdomain.host2.xml [L]
RewriteCond %{HTTP_HOST} ^www\.host3\.com [NC]
RewriteRule crossdomain.xml crossdomain.host3.xml [L]