Kudos to Ethicurean for taking a close look into whether organic chicken farms use more energy than conventional farms. They might, but before the cheerleaders of confined chicken production gloat, all sources point out that chickens are the one exception to the rule that organic farms use far less energy overall than their conventional counterparts. As Ethicurean quotes from one report:

Organic field crops and animal products generally consume less primary energy than non-organic counterparts owing to the use of legumes to fix [nitrogen] rather than fuel to make synthetic fertilisers. Poultry meat and eggs are exceptions, resulting from the very high efficiency of feed conversion in the non-organic sector.

Centralized chicken farming, however, is one of the reasons for pollution in places like the Chesapeake Bay in the mid-Atlantic region. Nitrogenous waste seeps from these chicken factories and into the bay, leading to algae blooms and dead zones. Essentially, sea life is choked off.

Truly organic chickens, out on pasture, do not produce as much waste in one locale simply because they are not massively concentrated. In other words, considering the energy quotient alone without regard to other issues only muddies the water further.