The red or brown specks that you sometimes find in farm eggs are called "blood spots" or "meat spots". These tiny spots are not harmful and are caused by the rupture of a blood vessel during formation of the egg. While some people my find them unappetizing, they will not affect the taste of the egg.
Commercial eggs found in the grocery store are candled to check for defects in the eggs. Typically, eggs with spots are not found in the supermarket; however, they are used in other commercial foods.
Contrary to popular belief, a blood spot in an egg does not mean that it has been fertilized.