This issue is certainly a hot topic in UK circles, and one I feel very strongly about - apologies for not picking it up here earlier, but I don't normally look at this section. Apologies too for what will be a long post.
Perhaps the main issue currently is the question of sea lice and their effect on sea trout (sea-run browns), although there are other worrying consequences of this industry also.
Sea lice occur naturally in coastal waters, and attach themselves to salmon returning from their open-ocean feeding grounds. The concentration of salmon in an inshore farm leads to huge numbers of lice and their eggs. A few lice on an adult salmon aren't a problem. However, the lice also attack salmon and sea trout smolts after they decend the rivers to go to sea. These small fish are very vulnerable, and it is at this stage that the damage is caused. Smolts have been found, severely emaciated and infested in some cases with hundreds of lice which quite literally eat them away. It is sea trout in particular that are vulnerable because they feed in coastal waters and so the lice persist on them. By contrast, once salmon have 'run the gauntlet' they go to the open sea where lice are not a problem, although this is not to say that there is not significant mortality of salmon smolts as well as they pass through. Once famous sea trout fisheries like Loch Maree in Scotland and Delphi in Ireland have seen their numbers reduced to a fraction of their former catches. There appears to be a direct link between the placing of salmon cages near a river mouth and fall-off of sea trout numbers - and when cages are 'fallowed', numbers improve again. Fishermen have seen this correlation for years, although the fish farmers have only just acknowledged that a link exists at all.
Sea lice are controlled in salmon farms using chemicals such as 'Nuvan'. This is highly toxic to other marine life (as well as carcinogenic to humans), and has been linked to severe fall-offs in invertebrate life around salmon cages.
Because salmon cages are generally located in areas of low tidal activity and little current, waste products (principally excrement and uneaten food) accumulate on the sea bed under the cages. This leads to areas of the sea bed being poisoned, and can cause the blooms of toxic algae which affect, for example, shellfish. In extreme cases it results in 'red tides' which kill all marine animal life across a wide area.
There are other diseases and parasites associated with farmed salmon. Infectious Salmon Anaemia (ISA) and Gyrodactylus salaris are two. These can be transferred into rivers. A number of Norwegian rivers have been treated for Gyrodactylus - this basically involves pouring poison into the headstreams to kill every fish in the river. The rivers can then be restocked with healthy fish. This, so far as I am aware, is the only way of eradicating this parasite once it is present in a system.
Occasionally large numbers of fish escape from farms. They will run up the nearest river and attempt to spawn. We are coming to understand more about the genetic integrity of individual populations of fish, adapted by natural selection over many generations to best suit their particular home river. And it is clear that a large number of 'alien' spawners in a river with already reduced numbers of native fish could dilute the genetic integrity of a population. These escaped fish can also carry the diseases mentioned above into the rivers.
There are a few deep water, open sea farms that get round some of the problems, but they all dump chemicals and waste into the sea in a way that would cause an outcry if it occurred on land. The only responsible way to farm fish is in inland tanks or ponds, with all waste water treated before being returned to its source. I'm afraid it's very much a case of 'out of sight, out of mind' as far as what happens in the sea is concerned.
There is a small campaign running currently to bring the problem of salmon farms to peoples' attention, led by well-known Scottish fisherman and writer Bruce Sandison. For more information, have a look at http://www.salmonfarmmonitor.org/