System operations may be defined as "totalizing structures that seek to explicate a phenomenon, behavior, or state in its entirety" (Bogost 6). They have a tendency to oversimplify the topics they are applied to, and leave very little room for secondary interpretation. This is contrasted with unit operations, which are more dynamic and complex interactions. For example, the Freudian notion that every action stems from an Oedipus Complex would be such a system operations, wheras accepting that behavior may be influenced by a variety of factors is more unit operational.
This idea is explored further in Unit Operations: An Approach to Videogame Criticism, by Ian Bogost.