These guidelines can be modified for evaluating birds and mammals.
Look at the facility in general. Is the building well maintained? Are electrical cords orderly or in a jumbled mess? Are products and shelves dusted?
Take a look at the animals. Do you see ticks or mites? Swollen eyes? Sunken eyes? Nasal discharge? Protruding hipbones? Is the vent area clean? Any gaping mouths? Do the animals seem listless?
Do the animals have enough room to stretch and move about? Are enclosures crowded ?
If there are mites, what type of treatment is used? Are new arrivals properly quarantined away from established animals? For how long?
Are the cages clean? It is easy to tell the difference between fresh and old feces. FRESH waste in couple enclosures is normal. No one can stand at hand with a pooper scooper after all. Old feces and excessive amounts of waste are not acceptable.
What type of heating and lighting are used? You need to know species requirements to accurately judge. You should not see hotrocks. Lots of 60w incandescent bulbs are another negative. Look for flourescent lighting required for aquatic turtles, iguanas, and other species. How often are flourescents replaced? The minimum is every 12 months, preferably every 6 to 9 months.
Are heating and lighting products in a place the animal can directly contact them? The animal should be able to come close but NOT in direct contact.
Is there a veterinarian involved ? To what extent?
Can they tell you if an animal was wild caught, captive born, or captive bred? Do they seem to care? Do they strive to deal only in captive bred animals?
If a store, do they sell a variety of appropriate supplies or do they have a limited selection of ineffective and inappropriate products?
A store with a high staff turnover or mainly teenaged staff often provides little or no training. I'm NOT saying teens cannot be knowledgeable, but in my experience stores with mainly high schoolers for staff have not been great stores.
How is the literature selection? A business selling a few outdated titles or none at all are most likely not keeping up with the latest in herp husbandry.