The concept of self-organisation is a very misunderstood topic when it comes to applying it to organisations.
Bas Reus is exploring what it means to say that humans are self-organising, over at http://basreus.nl/2009/07/27/self-organization-defined/#comment-51. His post outlines the development of his thinking in attempting to define self-orgnisation.
Arising from the study of complexity, the important thing about self-organisation is that the ordering of society (or people in organisations) occurs through local interaction in the absence of an overall blueprint or plan. As any top manager will tell you, you can’t just make a plan, tell others and then confidently expect that the plan will be followed. Instead, all sorts of unexpected things happen – people interpret things differently, they react to things in surprising ways and there are unintended consequences. This is what is meant by saying there is no overall blueprint or plan.