Check out the fascinating work of Philip H. Howard, Associate Professor, Michigan State University. Howard has produced a series of graphics showing the structure of the organic food industry. They depict the industry's consolidation over time, a trend which has often involved larger conventional food businesses acquiring smaller organic ones.
As of May 2013, the below national brands remain independently owned. There are many independent local and regional that are not listed, including Kalona SuperNatural, Cedar Summit, Whole Grain Milling, and many others.
The Wedge tries to indicate local companies on store shelves but lack of a sign does not mean that it is not local. Product labels indicate the location of companies. Ask Customer Service if you have questions.