What are the less obvious systems that affect the way people organise?

The Organisation Chart is a classic example. Organisation Charts are essentially diagrams of the Functional Command and Control Structure of Management.

If this is the only model used within an organisation to identify its structure, then it is more likely that the organisation will suffer from functional conflict or segregation, and relatively low satisfaction and morale of non-managerial staff (i.e. those who have the least control).