I think the solution to the pet stores isn't necessarily through boycotting them. Personally, I wouldn't set out to get a dog from one, but I can't say that if I walked into one and saw a yorkie sitting there all by his lonesome that I would be able to resist taking him home.
The solution to the problem lies within legislation. As long as their are laws that allow these practices to go on, there will be puppy mills and pet stores.
Unfortunately, politicians today have bigger issues on their plates than dealing with puppies in cages. Sigh.