DIY sanitization for eggs to incubate

Well as long as the eggs are clean without any significant poop on them, they are good to incubate. Some people do sanitize and wash every egg before incubation, but that is just completely unnecessary and can actually do damage to the egg. If there is poop on the eggs, feel free to wipe it off with a damp rag or paper towel though.

When an egg is laid, it is covered with a protective membrane enamel called the bloom, this protects the egg from dirt, pathogens and parasites from entering the egg. When the egg is washed, the bloom (protective coating) is destroyed and leaves the egg vulnerable to a number of things that could enter the egg and harm the developing embryo.

So you see...its best to leave the eggs unwashed unless you absolutely have to because of dirt or poop.

 

Fumigation of eggs and incubator is commonplace commercially

from http://msucares.com/poultry/reproductions/poultry_fumigate.html

Fumigation and sanitation of hatching eggs
Sanitize eggs and equipment before storage or use by fumigating. Under-fumigation does not kill the bacteria, but over- fumigation can kill the chick embryo in the egg. Use recommended amounts of chemicals at the right time for the length of time specified.
A room or cabinet large enough to hold the eggs is required. It must be relatively air tight and equipped with a small fan to circulate the gas. Calculate the inside volume of the structure by multiplying the inside length by the width by the height.

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Stack the eggs inside the room or cabinet on wire racks, in wire baskets, or on egg flats so air can circulate among the eggs. Remove eggs from the cases for good air circulation. Formaldehyde gas is produced by mixing 0.6 gram of potassium permanganate (KmnO4) with 1.2 cc of formalin (37.5 percent formaldehyde) for each cubic foot of space in the fumigating structure. Mix the ingredients in an earthenware or enamelware container with a capacity at least 10 times the total volume of the ingredients.
Circulate the gas within the structure for 20 minutes and then expel the gas. The temperature during fumigation should be above 70o F. Allow eggs to air out for several hours before placing them in cases.
Additional information on hatching egg sanitation and fumigation can be found inHatchery Management Guide and Care and Incubation of Hatching Eggs.