Does Nike operate and own Nike Town stores or does it have license
agreement with a third party?
Other examples of  brandflagship stores also welcome

Dear John, 

Niketown is operated directly by Nike: 

"Nike tested the concept of direct selling in the real world when they
opened their own NikeTown stores in the US in the early '90s."
(SOURCE: Mark Ashley-Wilson, "Old & new sales channels need to be
nurtured in the online era",
<http://www.bandt.com.au/news/be/0c002bbe.asp>).

Apple's flagship stores are also operated by Apple: 
Apple Store (retail) 
<http://en.wikipedia.org/wiki/Apple_Store_(retail)> 

I hope this answers your question. Please contact me if you need any
clarification on this answer before you rate it.

Thanks for the fast answer. The Apple part seems clear. In the Nike
article it isn't stated unambigously that the store is owned and
operated by Nike itself. I thought they might license out the
operations to another company. Like many companies do with their
manufacturing.