The problem with farmed fish (I'm thinking in particular salmon) is that they aren't eating their normal diet, they're crowded and much more stressed than their wild cousins. This means they're much more vulnerable to parasites and disease (and roaming jellyfish swarms), and they're fed dyes to give their flesh that pink color.
I don't know about other fish like tilapia, though.

Now I feel like I can't eat anything again. :|