One of the situations where the original question tends to pop up is one where you have some "stuff" that needs to be done after the interrupt occurs, but not inside the ISR since it takes too long and you need to allow other interrupts during this time.

A solution here is to put the "stuff" into a different, second ISR (one where you can trigger the appropriate interrupt by software) and set this interrupt to low priority. In the first ISR, you set the interrupt condition for the second ISR. Now other high-priority interrupts will be serviced, but the regular program execution is postponed until the second ISR is finished.