With all due humility I'd like to add a couple of things to this debate and explain my misgivings about farmed fish in particular, probably unnecessarily as my lovely wife has already made a better case than I ever could. Apologies in advance for a post that will inevitably be too long.
As Quentin said the main issues were- environmental impact, welfare, and sustainability. I would add a fourth - health.
-taking the health issue first: the 2004 research of Hites et al in Science which found dangerous levels of PCB's was based on a survey of 2 tonnes of atlantic salmon. Thats a lot of fish. The conclusion that US and Candian salmon should only be consumed once a month, and scottish salmon consumption would be best restricted to 3 meals a year, is based on the US Environmental Agency's idea of what is a safe level of PCB's (its in the order of 30 parts per billion i believe). Its worth noting that salmon farmers- generally employees of a handful of huge corporations who divvy up this multi billion pound industry- have so far been unable to produce any substantive (in fact I can't seem to find any at all) research to contradict these findings. Instead they use the FDA's 1984 assessment of 'safe' levels of PCB's (2000 parts per billion). Personally I'm not comfortable with that. Quentin was right that PCBs are present in a lot of what we eat but in farmed salmon the levels are unacceptably high in my opinion.
Nor am I comfortable with a food that has been treated with marine toxins like SLICE which is required to kill the plague like infestations of sea lice which infest cages (salmon were simply not built to exist in confined spaces throughout their life cycle). I don't much like the idea of my fish supper having rubbed its fins partially off on cages treated with anti fouling paints -usually Flexgard which is stored in containers marked 'toxic to acquatic organsisms). Another survey found that parasites like tapeworms have been passed on in Chilean farmed salmon when eaten raw. And I worry about antibiotics used on farmed salmon with unknown impact on those consuming the fish.
-Environmentally: salmon farming has a terrible environmental record and continues to cause significant and scary damage to the environment. Just a few of the issues: escaped fish (millions of them) outcompeting wild fish and diluting their gene pools not to mention spreading diseases to local wild populations; anti fouling chemicals used on the cages leave heavy metal residues (a 2007 survey found extremely high levels of copper and cadmium on sea beds benath farms);farm induced sea lice infestations have very probably caused the catastrophic decline of wild populations of migratory fish ...and we can go on (all of the health issues for humans consuming farmed salmon are played out in the acquatic life found in fjords and sea lochs where the farms are based- contaminated shellfish, algal blooms etc etc).
-Welfare: atlantic salmon are a migratory fish. in farms they are packed in, often allocated the equivalent of a bathtub of water each-its battery farming. To me its questionable at best but I think its the least of the problems.
-sustainability: taking 3 pounds of wild fish and rendering it into pellets to raise one pound of farmed salmon cannot, in my opinion, be sustainable. In a world of food shortages its insane.It decreases the net amount of protein . Anchovies and sand eels and all sorts of juvenile fish are being hoovered up to feed farmed salmon. Krill too now. These populations are being overfished in a way that is not sustainable. In fact one third of the total world catch is ground up into fsh meal (approx 30 million tonnes in 2007) and 3 5 million tonnes of that goes to feed salmon.
So Waitrose support a film which is all about overfishing while selling and indeed promoting a product which drives overfishing . Its more defensible on grounds of sustainability to eat a mature cod which has at least had time to breed in its life, than to eat farmed salmon.
Seabird populations appear to be in decline, and we know wild fsh populations are suffering on a number of fronts- salmon farming has to be making that worse.
Salmon can be raised with a lower ratio of wild fish in their feed but then the Omega 3 level starts dropping as Quentin himself pointed out.
I think Waitrose should be respected if not applauded for at least engaging in the debate (cf. Tescos, Sainsburys et al). Of course they are cashing in on a 'green' issue, using the film to give themselves an edge. Thats OK- if the film has provoked any change thats good news, but they need to be consistent, not just engage in token support, or take the convenient way out of what Quentin rightly said was a very complex debate.
Farming fish undoubtedly has a crucial role to play in the long term solution to the fishing crisis but salmon farming as currently practised is not part of the solution its a big pat of the crisis.
Sorry-gone on for far too long and I haven't even got started on farmed prawns!