iFlicks can trigger Apple Scripts from Rules as well. Due to sandboxing this option is limited and calling into many other Applications (like Finder) is denied by the Mac OS.
It is still possible to use the way of automatization for tasks like sending Prowl messages.
Other tasks that could be done here is closing iFlicks once the queue is empty or displaying messages.
Starting with iFlicks 2.0.3 it is also possible to pass the video that is processed to the Apple Script. This allows for a wide range of additional tasks to be performed. This is done by adding a action method to the script, which has the video as the sole parameter.
Note: This way of automatization should not be used to copy files to different locations or running other time consuming tasks. Instead of copying the files after processing the output folder can be set using the rules or by hand prior to processing.