I say ditto to what has been mentioned about friendly, knowledgable, helpful salespeople, cozy but not crowded fabric displays, name of pattern attached to each quilt or other item (tote or whatever) on display and patterns available for each, flexible hours, variety of classes/demos for quilters of all degress of expertise (clearly stated which level a particular class/demo is primarily geared to), nice clean restroom, comfortable place to sit, and some sort of play area for kids.
The place to sit and play area for kids can be really important for us babysitting grammys who shop two at a time with one or more little ones. My friend and I visited a new (to us) LQS in our general area - less than an hours drive - a short time ago. The sitting and play area only took up a very small space, but was such a treat. There were 2 comfy chairs, a small footstool and a basket of quilting magazines in the sitting area. The play area was on one of those rugs (24x36 I think but maybe as large as 36x48) with the streets printed on to run toy cars with a couple of cars, a small stuffed animal or two, and a little bookshelf with about a dozen or so books of a variety of reading levels. Very simple, but enjoyed greatly by the 5 y/o DGD we had with us. I especially enjoyed the sitting area as I had an infected foot that needed to be propped up while my friend continued shopping. We did not spend a lot that day but we will both be going back as time and finances allow.