Fabric Tales and Emico Fabrics are online shops that sells japanese fabric.
Found a set of wonderful Flickr images of Shinzi Katoh's work in retail shops.
Okadaya is a japanese online crafter shop whereas Fujisan is a online general shop-at least I think. :-)
Doishugei seems to be of a higher class and expensive selection of crafter shop, especially embroidery threads and supplies.
Still in learning stage and found that Clover is a craft tools and kit manufacturer that has interesting pages to explain uses and function of its products.
Lin Net is a cool japanese linen online shop - elegant and clean, enough to entice itchy crafter fingers to order.
BeinFait Make Matie is a name that is related to a magazine or catalog magazine available at most japanese bookstore - beautiful embrodery and needlework.
*Image from Fabric Tales