Encourage diversity within the farm. Choosing "poly culture" over "monoculture" results in less waste and often, reduced fossil fuel consumption.
Use varieties and breeds that are well-adapted to the conditions in your locale, rather than bred for maximum productivity and storage (with a sacrifice in hardiness and flavor).
Rotate crops and pasture. Use companion planting and green manures to keep the land perpetually fertile and to prevent topsoil loss. Don't let any one piece of land lose an irreplaceable amount of nutrients.
Keep plants and animals around that indirectly benefit the farm's stability and productivity. For example, yarrow and nettles add to the nutritional value of plants grown near them, as well as increase the volatile oil content of plants grown for oils. Plant extra basil to serve as an insecticide, and keep guinea fowl around to keep ticks at bay. As they roam your farm (and the surrounding countryside), guineas eat the ticks left by browsing deer off tall grasses. They are traditionally reputed to kill or keep rattlesnakes away as well.
If guinea fowls are not common to your area, try growing ducks (if you have a fish pond) and/or chickens. Chickens can eat crop trimmings and vegetable waste. If they can't eat them all, they claw and step on it, enough to make it into organic fertilizers rich in nitrogen (especially when added to their poop).
Raise both livestock and crops, and set up a mutually beneficial relationship between them. The simplest way to do this is to use manure from your livestock to fertilize crops, and use some of your crops to feed the livestock. If you are unable to raise both, find a neighbor who's specializing in the opposite and set up an exchange.