UC Davis, those smarties down in California, just released a 10-year study comparing the "Influence of Organic and Conventional Crop Management Practices on the Content of Flavonoids in Tomatoes". Flavonoids are "plant secondary metabolites" and are commonly known for their antioxidant qualities. They also help the plant produce pigment which in turn attracts polliantors. You know, all the good stuff. You can read the study here, but in essence organic tomatoes contain higher levels of minerals. The study compared conventionally grown fruits to those grown on organic plots over the course of 10 (!) years, and noted the nutritent content. If you take the time to read, you will note that they attribute this to increased amounts of organic matter in the soil, and the decreased need to add manures (ie fertilizer) to the gardens.
This is exactly what I encourage urban gardeners to do at home - practice crop rotation!! And build up your soil. It really does pay in the long run. Even those fancy scientists agree.