I guess the answer will be different depending on which country/ part of the world you are in! Here in Europe, I like The Cotton Patch www.cottonpatch.co.uk and also Fabric Warehouse www.fabricwarehouse.co.uk.
Spotlight always has a great range of craft fabrics, and many can also be purchased online. Etsy is another great website, with gorgeous fabric from all around the world.
Another lesser-known online shop is Alie Jane, which is based in Newcastle...the Australian one! They stock a great range of lovely and unusual Japanese craft fabrics. In the UK, Liberty also has some gorgeous craft fabrics, many which are classic vintage designs.