You can pretty much guarantee that non-organic feed has the residues of pesticides and probably herbicides in it. GMOs in crop plants are not necessarily bad in my opinion; it's the herbicides that get sprayed on some of those GMO crops that I take issue with. The plants (mosst of which are made by Monsanto) have been engineered to carry herbicide-resistance genes, so a farmer can spray the entire crop with herbicides to kill the weeds. Pesticide and herbicide residues in chicken feed end up in eggs, and in the bodies of whomever eats the eggs. I don't trust what the USDA says about what levels of these things are safe in the body - the agency really works for big agriculture companies like Monsanto and not for consumers - and the FDA has no power to regulate this stuff anymore. For example, atrazine and some of the other chemicals commonly used by non-organic farmers are estrogen analogs, which means they definitely affect animal bodies. There is a bunch of research that proves the effects, and some of them are quite visible (check out the hermaphroditic frogs in streams with agricultural runoff). The debate about whether to ban the use of estrogen analogs in agriculture has gone on for decades, just like the similar debate about DDT and other chemicals that are now considered too dangerous to use.
But even beyond the personal health issues, the scale of food production in this country is having global effects that I don't like. For example, Monsanto has a virtual monopoly on corn and soy seed, and apparently uses strong-arm tactics on large-scale farmers that don't use their seed. Even aside from the herbicide-drenched Monsanto GMOs, I do not want agriculture companies to control farmers, so I will go out of my way not to buy products that have been produced using Monsanto products. I also think the control wielded over Washington by large food companies is resulting in policies that are damaging our bodies and our environment, so I also go out of my way to avoid the products of large food companies. Is it a pain to shop like this? Incredibly. Do I personally have an impact on these large issues? Not a bit. But if enough of us consumers take a stand on this something might change, so I'm in.