With Configuration Manager 2007 Integration in App-V 4.6, there was a very popular feature that allowed for what we refer to as “implicit uninstall.” This means that when a user is no longer part of collection, the virtual applications advertised to them would then be removed. This was very easy to configure by selecting “Remove this virtual application when it is no longer advertised” when importing the virtual application. This meant the client would uninstall the virtual application if they are removed from the target collection.
This exact feature is not implemented this exact same way with Configuration Manager 2012. The APP-V 5/Configuration Manager 2012 Integration whitepaper has been updated to include a methodology for achieving this same effect through custom collections – both through the console or through WQL.
Page 30 of the updated Configuration Manager White Paper discusses this: