First up is the alley cropping method.
In this method you plant trees in two row, and you plant crops in between the trees. You then prune/cut the leaves of the trees and let the materials form the tree to spread over the crops, which helps the soil quality and increases production.
http://nac.unl.edu/documents/workingtrees/infosheets/WT_Info_alley_cropping.pdf
The second one is the Perennial root systems. It basically uses perennial seed which last year around, which helps the soil, and causes less pollution.
http://ngm.nationalgeographic.com/2011/04/big-idea/perennial-grains-text
http://guilford.ces.ncsu.edu/2012/08/fall-is-for-planting-and-dividing-perennials/
Other Design Ideas(though not reliable source):