Two in the Houston area:
Guitar Hacienda in League City. Excellent selection of acoustics, including particularly Taylors and Martins. They also carry McPhersons if anybody is into that (I am!). They are a fairly small shop though so they're not a Gibson dealer. Also, Danny there is a mighty fine tech and will set up any instrument to your specs...whether you buy it from him or from somewhere else.
Fuller's Vintage in Houston. Huge selection of acoustics and electrics, including Martin, Taylor and Gibson. What really sets them apart are the high end instruments they regularly stock. Especially the Gibsons...like new ES335s, 355s, L5s, 175s, 165s, you get the picture. I've dropped lots of money there. Probably more than I should have over the years. Fuller's doesn't really do a set-up, so if you buy something in need of that (as most Gibsons do) you will have to go somewhere else to have it done. I have my favorites, and Danny (see above) is one. Ron Pace in Houston is the other. But I suppose that's a different thread.
And of course, fine folks to deal with at both shops. Somebody's already mentioned Great Southern. Been there too. Nice folks, and they do a good job with a set-up, but their stock isn't generally close to GH or Fullers.