Guitar Center is for sure my favorite. They have the best selection and are very knowledgeable about the finer details of guitar craftsmanship. Their stores are full of customers who appreciate music and are very considerate of the instruments they handle and to others around them.
HAHAHAHAHAHA! Just kidding, of course. Ugh. Below are three stores I have bought from, none of which are actually local to me:
MUSIC VILLA, Bozeman, Montana: I have purchased both my 712 and my custom Koa here, both after much time spent with Joe (who does most of the store's demos on YouTube) and with the owner, Paul. They have the feel and philosophy of a small-town store and truly seem to care about the customer's relationship with music. They always throw in extra merchandise with orders and host local events in their communities. Very pleasant and professional.
SHORELINE MUSIC, Durango Colorado: I purchased my Custom GC from John, the owner, after it was announced that cocobolo would apparently become hard to come by. John spent an awful lot of time helping me make a decision but our conversations also tended to drift to many unrelated topics. I have also purchased pick-ups, strings, and other gear from there, and John always includes a hand-written note when he ships the merchandise.
EDDIE'S GUITARS, Maplewood, Missouri: I recently bought a used Lowden F35 guitar from Matt Chukla, who is the acoustic guitar salesperson and a hell of a guitar player in his own right. They are a small operation (I believe only 8 employees) but Matt was very patient and helpful throughout the process. He even understated the condition of the guitar, which was in truly mint condition and looked brand new when it arrived.