It is very important that you never wash eggs (especially cold water) as this removes the natural antibacterial coating on egg shells. If you are using cold water, this causes the egg inside to shrink slightly and allow even more bacteria to pass through the shell into the egg cavity. Commercially, it is standard to either dry brush them as soon as possible - or to wash them quickly in warm water and immediately spray on a sanitiser. Organic eggs are always dry scrubbed and hence a slightly dirty look.
It is best to avoid the eggs getting dirty in the first place. This is done by collecting the eggs more often to avoid soiling and trampling.