Agriculture vs. Sustainability

I work at a restaurant that is has been growing as a name that serves sustainable fish, and so it is something I find myself encountering quite a bit.  I was always happy to just absorb whatever people around me at work had to say about it, but today I decided to research it a bit and form some opinions myself.  Words like "farm-raised" and "wild-caught" are thrown around a lot, and there is a lot of hype about both of these options.
Wild-caught fish generally has a much better reputation because there are some (this may not be the nicest way to say it) pretty nasty fish farms out there.  I have heard and read many things about fish in farms being fed things that are potentially toxic, not being given enough space, and generally living in conditions that do not mimic the wild as much as the owners of these farms would like you to think.  However, there are some farms that are starting to pop up, mostly in the UK, that are not entirely horrible for the environment.  They have different standards of circulating the water, and they also tend to rotate the fish through three tanks, which is preferable to keeping them in the same tank all the time.
On the other hand, wild-caught fish, when the fish is something that is appropriate to catch and is not on any type of endangered list, generally has a much better reputation.  There are many reasons for this.  Farms that raise fish can try and mimic natural conditions, but there is just nothing like the real thing.  Also, it is difficult to regulate a man-made environment.  Even though farms sometimes have more than one type of fish, this can also lead to one type taking over the rest because of an ill-regulated environment.
The Monterrey Bay Aquarium Seafood Guide is widely recognized at providing the public with up-to-date descriptions of which fish are the best to eat.  They have a system that represents the sustainability of a fish choice.  Their "green light" is the best choice, the "yellow light" is a good alternative, and a "red light" is something that is not sustainable, or in danger of being overfished, and so it should not be used.  They update this guide every six months and it is very user-friendly, so much so that they even have an iPhone app!