it's that it hasn't been doused in pesticides and other poisonous chemicals... stuff that even a thourough wash doesn't get off.
Stuff thats in a shell of some sort i'm less spicky about. say, sweet potatoes, bananas, oranges, etc ... I peel them. But spinach and other greens, mushrooms, where it is directly exposed to the sprays, I try to avoid conventional foods. and of course, there's always the soil itself that feeds the plants, and it does effect the food. Maybe not in terms of nutrient content, but in terms of chemical intake.