I guess this is an odd thread to make my first post in, but you gotta start somewhere right?
Anyway, there's a couple of reasons I personally like to buy from a LFS as opposed to a "chain" store. First, there are more reasons than one they call Petcos and Petsmarts chain stores. Aside from the obvious fact that they have multiple locations across the country, their aquariums are basically one giant divided tank. It's a huge system that circulates the same water through all the tanks. If they add a diseased fish in one tank, the same water that fish swims in will eventually make it's way into the same tank your new fish was in. There is a Petsmart not far from here that I can always count on having parasites, regardless of the type of fish. The LFS usually has individual tanks. Although illnesses are still very possible from a LFS, they can at least isolate a sick tank.
The second reason is I would MUCH rather pay a little extra and support the little guy. He's basically one guy competing against giant companies. Even if he is 15% higher or so, big deal. The little guy is usually the one you can count on for the best selection, best quality fish, and overall customer service.
Case in point: Not long ago I was in the local LFS and noticed a dead common pleco in a tank that another customer had just picked out a fish from. All the other fish looked very healthy. The employee apparently didn't see the dead fish. I quietly pointed it out to him when the other customer wasn't looking, and he proceeded to dump the healthy fish he had just netted back into the tank. He wiped off the price tag from the tank, and told the other customer he would have to pick out another fish from a different tank. This one was going back under quarantine for a week to see how the other fish do. The LFS risked loosing that one sale in the interest of making sure their stock was healthy. That same LFS also got in a huge, 500+ , shipment of Cardinal Tetras about a month ago. I think about 300 of those were spoken for before the shipment arrived, but he still wouldn't sell any to me or any other customer until they had been in quarantine for several weeks until the owner was satisfied the fish were healthy and they had acclimated properly. You'll never find a chain store that does that.
My point is that the little guy is the one who provides a quality of service that the big chain stores can't even begin to match.
Didn't mean for my first post to be a soapbox rant, but I'm a BIG supporter of small business.