A Quilted Heart in Vacaville on Alamo Drive is a nice place - they also sell sewing machines so the store itself is a mixed bag - but the staff is fun.
Pincushion Boutique is a classy place in Davis on 2nd Street (a little tricky to find but worth it)
The Fabric Garden in Sacramento on Fulton Ave is one I go to regularly. Friendly staff and a nice selection of fabric.