This is one of the reasons we moved to Durham! I did not want to end up in a wasteland of big, brand name grocery stores.
Granted Whole Foods is in itself becoming very corporate, but they are more dedicated to offering organic items, they label all locally produced items so you can buy local where possible; and the philosophy is more whole.
We like the sandwich bar which is not known about by many. You have to go to the deli counter and fill out a little slip of paper and hand it to a deli member. They will then make you a sandwich to order, you choose bread, fillings, toppings and condiments. Great for an impromptu picnic.
Of course produce and all other products (bulk items, spices and teas) are great. Only problem is the store is small and limited in space so we often have to be patient with the stocking.
I also like supporting Earth Fare and Weaver Street Market. The Durham Food Coop needs alot of TLC, so although I like the thought of supporting them, they have a ways to go before you can really get some serious shopping done there.