Like someone mentioned before, much of the negative attitude towards salmon farming comes directly from the commercial fishing industry, which is very powerful as you might know if you're a sport fisherperson. Granted, there are some biases coming from the other side of the spectrum as well.
Yes, it's a fact, wild fish contain higher amounts of certain chemicals, including PCBs which are highly carcinogenic.
Feed is NOT wasted. Feed costs $18-$25 dollars for a 50lbs. bag. When you're feeding hundreds or thousands of pounds a day, you're not going to want to waste any. Feed is the largest expense in any aquaculture setting.
Farmed salmon are rarely fed antibiotics. Again, cost is an issue. I'm sure some of you have had to get antibiotics from the pharmacy before. Was it cheap? Farmed fish use the same types of antibiotics that we do in some cases. Farmed fish don't generally get viral or bacterial infections because they're healthy, and in many cases, in better shape than wild fish.
Yes, waste from net pen operations can be large, but let's look at this on the broad scale: How much nitrogen and phosphorus is leaching into Lake Washington from beachfront McMansions? How many of you live alongside a river? If you do, you're polluting... a lot. All W. Washington towns pump treated sewage directly into the Sound. The treatment plants can only do so good of a job...
My 2 cents.