In my mind, the mark of a good gun shop is one that prices a gun fairly to begin with. I look at MSRP, I look at Gun Broker, and then I call 5-10 shops to see what prices they are offering. Takes all of 30 minutes to do this.
I think one of the best gun shops I've dealt with from an inventory/knowledge/price standpoint is Plainfield Shooting Supply. The only complaint I have is their ammo prices are higher than I like to pay, but then again, who but Wal-Mart has cheap ammo now-a-days?
Agreed... and most of my gun purchases go to PSS, and most of my local accessory purchases go to Bradis for just those reasons.