Some great bookstores can be found north of the city in Petaluma and Santa Rosa. Classic junk shop with everything from books to old postcards to used veding machines. One of my favorite places in the city. More upscale thrift store aimed at twenty-somthings and club kids. There is some good stuff to be found all the same.
All sales benefit various local charities.
Big store with emphasis on furniture and clothing. Salvage, desks, furniture, books, everything. The collection of toilets in the yard can be mind-boggling. New and used. If you want a good record store, you gotta go to Berkeley.