If you're carefull and know how to pick fish, store bought can be fine. My clown loaches, original angels, harlequin rasboras, and otocinclus were all store bought Mostly from Petsmart, a few from Petco. I had no problems with them.
Lately, I've been buying fish from breeders, since they are allot cheaper. Breeders usually can answer any health/fish issues you have and they will usually help you in case you have any problems.
Keep in mind...
1. When buying fish from stores, make sure you buy fish a few days after the fish are received from the store. This gives the fish a chance to relax after allot of stress from shipment and a new environment.
2. When you do intend to buy fish from the store, visit the store the next couple of days and observe the fishes and/or inhabitants in the tank. This gives you a chance to make sure the fish and it's tankmates look healthy.
3. When bringing fish home, you should QT the fish for a couple of weeks to acclimate them to your water parameters and to observe them to make sure they are ok.