I like Trader Joe's to stock up on things like canned beans and soups, frozen veggies, soy milk, etc. as they do have great prices. I agree about the produce though, most of the time it is not that good.

I go to Whole Foods once in a while for things that I can't get anywhere else, but the prices are too high for most shopping. Most of the time I go to local stores with good selection of natural foods, I generally avoid the big chains.

There is a farm store with nice produce, lots of lentils and beans, etc. that is ~7 miles away, I do a lot of shopping there on my bike.