Glad Creations, not too far from downtown Minneapolis:
http://www.gladcreationsquilts.com/ . This shop has been around for at least 20 years. It is small but packed to the gills with batiks, really good quality fabrics, patterns, etc. This shop has a somewhat traditional bent.
Twin Cities Quilting in Roseville, a suburb of St. Paul:
http://twincitiesquilting.com/TCQ/Welcome.html . This is a newer shop, only been around for about 2 years, and not as packed with stuff as Glad. Has more of a modern twist to its patterns and ideas.
S.R. Harris is a cut-your-own fabric warehouse that is huge. They have a section of batiks on rolls (mostly Timeless Treasures) and a large variety of cottons. They also have silks, novelty fabrics, home dec fabrics and trims, anything you can think of in fabric. You measure and cut your own fabrics, write yardage and bolt price on a sticker you slap on the fabric. When you get to checkout, everything is 50% off the bolt price. Last time I was there, over a year ago, the TT batiks came to $7/yd.
http://www.srharrisfabric.com/
I haven't been there, but I believe there is a shop called My Blue Bamboo located in Plymouth, a suburb of Minneapolis (at least, that is the headquarters for their online catalog):
http://www.mybluebamboo.com/
Edit: The Mill End Textiles outlets (fabric) seem to vary greatly in quality depending on location. Some seem to specialize in specific fabrics and/or in flat folds.