Software Prototyping is most useful in development of systems having high level of user interactions such as online systems. Systems which need users to fill out forms or go through various screens before data is processed can use prototyping very effectively to give the exact look and feel even before the actual software is developed.
Software that involves too much of data processing and most of the functionality is internal with very little user interface does not usually benefit from prototyping. Prototype development could be an extra overhead in such projects and may need lot of extra efforts.