This is based on USDA testing and it's based on how people usually eat the fruit or veg. For example, a melon would be be eaten without the peel, while an apple might be eaten with the peel, so the peel isn't included in the test for the melon, but probably is for apples.
I even have their app on my phone: Summary | EWG's 2013 Shopper's Guide to Pesticides in Produce™. A lot of the fruit and veg I buy is organic. I like this list because I can check what I don't mind buying in the not-organic version, like onions and cabbage.