Of all of those mentioned already, I really like the Fabric Shack. They have an entire room of wonderful flannel as well as other regular quilting cottons. The notions section downstairs is a great resource as well.
Another shop I was at a couple of years ago is Dutchland Quilt Patch
http://www.dutchlandquilts.com/about. I was very pleased with their selection and prices. Enough that I bought 16.5 yards of fabric there! I was at the Intercourse, PA location. Huge selection including, at the time, quite an extensive selection of civil war repros.
I miss Old Country. Was definitely a 'must stop'.