I go to Hobby Lobby for Kona solids and sometimes they just have the cutest prints, and one LQS that is almost exclusively Moda fabrics. The vast majority of what I buy is online.
www.fatquartershop.com is my favorite.
www.hancocksofpaducah.com - I just ordered for the first time recently. Probably won't again. A full 7 days between ordering and shipping is unacceptable to me.
www.fabricworm.com - They create their own coordinating FQ bundles by mixing and matching different designers and collections. It's a great idea and I have loved their selection and service.
www.connectingthreads.com - Don't love their fabric, but will be ordering thread from them soon.
www.fabricseeds.com has just about the cheapest pre-cut prices around and incredibly fast shipping.