Everyone's hit on great points already with the no dead/unhealthy fish, presentable non-bare tanks, knowledgable employees, etc, so here's one that I haven't seen called out yet...
Bettas. These are often one of the biggest indicators of how good a LFS is for me because they are so tolerant of being mistreated that they're usually the first place a store will cut corners. Besides the obvious of whether any are dead or dying, how do they keep them? Are they packed together on a shelf in tiny cups? Or are they integrated into the other display tanks so they have socialization and space to keep their swimming muscles in shape? A betta that is being kept in a tank with other fish will always tend to be more willing to accept other tankmates when you bring it home and will not struggle or sicken easily when subjected to anything other than dead calm water more than a couple inches deep.
It may seem overkill to judge a store based on one fish type, but this is hugely telling of their general store practices and care level.
