I, too would highly recommend Batiks Etc. and Sew What Fabrics. I've purchased from them several times and their service is great. Their prices are pretty good, too. I haven't been to their store, but they had a large booth at the AQS show in Knoxville that was fantastic. I definitely plan to stop at their store the next time we travel up I-81 to visit my DD in Maryland.
I've also recently made some purchases from Batiks Plus. They have great stock, but their prices are a little higher. Another shop with lots of batiks at good prices is Stitch-n-Frame. They are in Mississippi and nearly always have several lines of batiks on their Thursday Special.