I'd wonder if the behavioral problems are genetic or environmental; I can't think of anything that would be more maddening to an intelligent animal than the sterile environment of a cage.
The ones I mentioned are due to genetics (though genes of course can react with environmental factors). Generalized stress signs in mice tend to be things like barbering, patterned behaviors, fighting, etc. These too though can be more prevalent and/or occur regardless of environment in certain strains. In some strains things like over barbering are bred for to act as models for certain human conditions, so I tried to specify that the things mentioned previously were not intentionally bred in to the strain.
There are actually different branches of research, and the guidelines and general culture can differ quite a bit. At most universities, the shift has been towards greater enrichment and greater choice. This includes training animals to, say, offer a leg for blood tests in return for a treat versus using something like a squeeze chute. This too includes better environments for rats and mice, with a focus on removing signs of stress behaviors. At my place of work, the rodents are cared for better than most people's pets, so it is easier to see the differences in strains, and they can be quite stark indeed.
Fowlman, mammals can have structural and behavioral changes based on things like color and pattern as well. The fascinating study on domesticating foxes covered that a bit, and there was an interesting talk I recently attended about dogs that was on a similar topic that I will see if there is any online presence for.
And Kiniska, you totally got the transgenics right. Oh man, did you ever!
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People do not have to agree, of course. However, the rules promote maintaining a friendly and educational atmosphere, and I generally find this encourages better debate and opportunities to educate, whereas people can be turned off entire causes (ie. 'preserving heritage breeds') when points are too forcefully or rudely made.
