An interesting topic -
after reading all that I can find on the subject I have formed an opinion that on the whole I would rather that the housewives of North American serve their families framed salmon rather than commerically caught salmon.
First regarding the PCBs found in farmed and wild salmon. While the commerical industry has made much of the fact the wild salmon have much lower PCB content that farmed fish. This is correct but ignores that not all salmon species are the same. For example the wild salmon that were found to have low PCB content were pinks and chums (other work indicates that sockeye have low levels as well) however as the article quote says wild chinook have levels which can at times exceed that of framed salmon. The reason of course is diet. The farmed fish and the wild chinook feed higher up on the food chain than pinks and chums. The bait fish (whether in the commerical fish food or those eaten by free swimmng salmon) concentrate the contaminates in their diet which in turn are concentrated as the salmon eat them. The pinks and chums feeding primarily at the same trophic level as the bait fish. Those chinook mostly likely to have contaminate levels are those with high fat content (springs, Copper river, etc -the PCB are concentrated in the animals fats) and the larger -older fish. The very large chinook have 4 to 6 years in which the PCB can build up.
The concern about the bait fish that farmed fish consume is another issue that is often raised. The real problem here is that we in the developed countries insist in consuming our protein in meats from animals in upper tropic levels (beef, chicken, salmon, etc). If we would confine our take of protein from soy and fish meal there would much more to go around. I don't expect that to happen any time soon. That said farmed fish will produce more pounds of protein for a given amount of feed than a wild fish. Unless we are willing to change our diets consuming farmed salmon is a more efficient human use of the forage resource.
While I share the concerns with diseases/sea lice and escapees from the net pen operations these impacts tend to be local. While we should continue to work to reduce those impacts I believe that even at current levels those envirnomental impacts are less than other sources protein - the beef and chicken industries and the impacts from commerical fishing. The impacts from say beef grazing and feed lots on the terrestial and aquatic envirnoments should be apparent to all. Commerical salmon impacts are widespread and include such things as by-catch issues in net fisheries, selection against larger, older and faster growing individuals in the population by net and hook and line fisheries.
In short as long as the human race continues to population the earth at current or large levels and we continue to insist on the luxury of taking our protein from high tropic levels we will be faced with the unpleasant task of choosing from poor choices. In this case for me at least the marketing of farmed salmon is a lesser evil than marketing commerically caught wild (free swimming) salmon.