Are you thinking purely of the nutritional advantages when choosing your foods, or do you also consider the impact on the environment or ethics of industrialized agriculture when making your choices?
I've been reading lately about the effects commercial farming has on the environment, and it's quite disturbing. The environment and even animal welfare suffer to an extent that is unimaginable. It's not just about how eating whole is better for our health.
The book "Six Arguments for a Greener Diet", by Michael Jacobson of the CSPI, provides some alarming statistics. For example,
..8,500 square miles - The size of the "dead zone" created in the Gulf of Mexico by fertilizer runoff carried by the Mississippi from the Upper Midwest.
..33 million - The number of cars needed to produce the same level of global warming as is caused by the methane gass emitted by livestock and their manure.
0.5 square feet - the amount of space allotted to the average layer hen.
4,500 gallons - the rain and irrigation water needed to produce a quarter pound of raw beef
17 trillion gallons - the amount of irrigation water used annually to produce feed for U.S. livestock
5 tons - the soil lost annually to erosion on an average acre of cropland
1 pound - the amount of fertilizer needed to produce 3 pounds of cooked beef
The book includes many more statistics, and details the various ways the environment is harmed by industrialized agriculture, mainly commercial beef, poultry, and dairy industries. There are the effects on the environment to consider, as well as the ethical treatment of the animals which are tortured their whole lives. This is not necessarily a plea for vegetarianism, but implies a need for less harmful methods of farming and ethical raising of livestock. I can't even buy milk or cheese anymore unless it comes from small dairies that let their cattle graze naturally.
Even sugar is as much an environmental concern as it is a health issue. Many people will still consume sugar in moderation, to avoid artificial sweeteners or HFCS, which should be ok. However, the production of sugar cane and beet sugar is one of the largest causes of deforestation and soil erosion on the planet. In the Phillippines alone, sugar production has resulted in a loss of a third to a half of the known species of snail and birds in the Philippines.
I recently read on CNN that we will not have seafood to eat in 40 years, due to human impact on the ecosystem. Water pollution, overfishing, and habitat destruction.
Does anyone else share these concerns, or am I becoming a worry-wart?

I googled this and have just read some horrifying articles about the cocoa slave trade. I'm so shocked that this goes on 
Nowadays I eat fish from time to time.