As a store owner I can tell you that this is one topic that interests me greatly. Since my specialty is reptiles I can speak with greater knowledge to that subject than to aquatics but I can only imagine that there are many similarities. I will also apologize in advance as I think it is going to be a slow day in the store and feel like typing so I think this will probably get a little long. Stop reading now or hold your tongue later. You have been warned.
WC vs Tank raised (captive bred is the reptile term) As some have pointed out, there are pluses and minuses for both.
Tank raised generally are more healthy but that is limited to the effects of hormones and other treatments the animals receive. TR can suffer the negative effects of severe inbreeding and other manipulation (hormones etc.) just as WCs can benefit greatly from appropriate preventive medical treatment and intervention. True tank raised, hobbiest bred if you will, provided that inbreeding and other aspects are addressed, are in almost all cases going to be healthier or at least adapt better to captivity. Farm raised fish on the other hand can have worse survival rates than their WC counterparts. Overcrowded conditions, exposure to unfamiliar parasites and diseases (ie. a SA tetra raised in an open pond in Singapore) can make many farm raised fish a risky proposition. I've seen articles that claim a very high percentage of farm raised guppies carry a certain type of bacteria that is not present in wild forms (I'll address the difference between these forms next.) so that jsut becasue a fish is tank, or farm, raised does not necessarily mean that it is healthier. Also, fish raised in the Far East have to travel longer and further to get to you than many closer South American WC specimens.
WC's can have decimating effects on wild populations but I would venture to guess that as a whole habitat destruction has far more of an impact than collection for the pet trade. While that doesn't minimize the effect of the pet trade nor let them off the hook, I think many animal rights groups tend to over stress the impact of the pet trade to help further their cause. It is much easier to convince those with deep pockets (read as potential financial contributor) that we should ban the import of a particular animal because they are all being collected for pets rather than try to convince them that we should do everything we can to help ensure that the natives don't cut down the forests or dam the rivers because that just may be considered a necessary evil for the native's survival. On the other hand TR specimens are often times bred to the point where they have little resemblance to their wild relatives and would certainly render them unsuitable for release into the wild (see the guppy example from above) which should put to rest any "we are saving the species" talk. You may be keeping the species alive in captivity but it is certainly not going to be suited for survival in the wild.
WC's are an important source of income for many natives. Though the amounts they receive may be paltry compared to the final cost of the fish in the trade, it does provide them with a means to make a living and this in turn provides them an incentive to at least consider a more conservative approach to harvest. Take away that incentive and the animals become something that is no longer of any use to them and all conservation efforts will either stop completely or at least be decreased by a substantial amount. Case in point, the Prehensile tailed skink. These residents of the Solomon islands reside high in the tree tops. The natives cut the trees down for firewood or whatever and as a result they come in contact with the lizards. In the past they either put the lizards in the dinner pot or shipped them off to an animal dealer to be exported. Either way they benefited. The Government banned the export of the animals so the only use they are to the natives now are as food. As one guy put it 10% surviving in the pet trade is better than 0% surviving in the cooking pot. Of course an argument to that might be at least those who died and got eaten were put to use rather than those who died for no other reason than to be put in a cage somewhere.
Many fish are available as TR and WC. Often side by side at my fish wholesaler. I will choose the TR if I have a choice but as pointed out they usually cost more and in this day of near $4.00 gallon gas prices (in the US) people do what they can to save money. If I buy the TR and sell the for $3.00 each and the guy across town buys the WC and sells them for $2.00 people will wonder why I am ripping them off. Of course its my responsibility to point out the difference but many people don't give me the chance.
WC does have a position in the hobby for new breeding stock as well. We all know the potential harmful effects of inbreeding. If you can outcross your stock with some new blood occasionally than that can only be a good thing, unless you are working toward a line bred trait but then I think we are talking about a different ballgame. I also think that Joe Average breeding cichlids in his basement would benefit more from the infusion of new blood than a huge fish farm in SE Asia. Well, maybe benefit might not be the best term, maybe I should say be interested in.
The thing that bothers me the most about WC is all the animals, be they fish, reptiles, birds, or what have you, is the importation of those species with dismal survival rates. I am not so familiar with any FW examples so I will use a few example from the SW trade and the reptile trade. Leopard wrasses and blue ribbon eels. Almost every book will tell you that these two species make very poor captives and yet they are collected for the pet trade in large numbers. As for reptiles, the Mandarin rat snake is a prime example $500.00 CB babies are wonderfully hardy and very beautiful snakes. The $50.00 WC adults may have a 10% chance at survival at best. They just do not adapt well to captivity. This is an example of price being a prime motivator as it is in most instances when dealing with live animals as pets.
On the flip side of this however, and again I will use the reptile trade as I am much more familiar with it, is the case of the flying dragon or Draco lizard, and the Mt. horned dragon. Both are species with abysmal survival records. Still they are imported by the thousands. However, thanks to the dedication of a few individuals these animals are being bred in captivity, for the second and third generations and perhaps even more. Had the importation of these animals been stopped these inroads to captive husbandry would not have been possible. Granted, they would not have been needed but now, even the WCs have a much better chance at survival because of the dedicated work of a few people have gained insight on what these animals need to survive. I'm sure there are plenty of example in the FW fish trade of fish that were, not so long ago, considered nearly impossible to keep but are now considered common, or if not common at least keepable.
As for the preference of a fish to be in the wild over being in a tank, that is something that we can not now and most likely will never be able to answer. Would you give up the freedom to live in a large city where you have the the room to roam wherever you may choose for a more secluded life free from the dangers of being shot by a stranger in a drive by shooting. Some people would and some wouldn't but the operative word there is people. These are not people, these are fish. You can not use the same argument. You are applying human emotions to non-human animals and assuming that they have the same responses. Of course, we also do not know that they do not have the same emotions and responses so some people would decide to ere on the side of caution. Its a fine line. You also can't use the argument that TR fish are acceptable and WC are not because TR fish have not been in the wild so they don't know what they are missing but that a wild fish will somehow be depressed by not being free any more. If you consider it unfair to deprive a WC fish of its natural habitat what makes it OK to not give TR specimen that same freedom. Using this logic it would be OK to raise a human in a 8X8 cell if he was born there in the first place because he doesn't know anything else.
The last issue I will discuss is simply what I call the want factor. Some people just want certain fish, and certain fish are not available as tank raised. Should they be told they can not have them if it has been shown that collection of that fish from the wild can be done in a safe, economical and ecologically sound manner.
As you can probably tell I do not have very strong opinions on this one way or the other. I can see the issues on both sides and I can respect the opinions of others. The main issue I see is not one of WC vs TR it is more a matter of the care the animal receives regardless of it's origin. Some people will do everything in their power to keep a WC specimen alive or they will forgo getting it. Others shouldn't be allowed to keep pet rocks even if they are tank raised.