Hi,
if you want to make all services in your server public, except those within a particular folder, do the following:
-Open ArcGIS Server Manager and log with Administrative privileges
-Click on the locker icon sitting by the name of the folder you want to make private
-Select the roles that you want to have access to that folder (you may need to create the roles first, or configure your identity store)
-Go into the Services Directory to make sure that the folder does no longer show for 'anonymous' users.
-Use the login link in the top-right corner of Services Directory to make sure that users form the role/s you define actually have access to the services in that particular role.
The trick is that ArcGIS 10.1 for Server always has security enabled (as opposed to previous versions). By default we make all services public, meaning that anyone can access them, but you can easily make them private at any time.
Ismael