I'm creating all of my APM alerts to use APM-Application since it's easy to manage and maintain. I don't like the idea of adding or removing a monitor to an application and then having to update the corresponding alert profile. The only snag I'm running into with APM-Application is that my sysadmins want to know which monitor for the application is down. This would help them better know how to respond but would be a tremendous amount of work to create and mange in a APM-Monitor alerting style just to give them that additional information.
