I think perhaps for a general good range, Elizabeths is a good place to start though now that I work in an op shop I have not been here for several years -there also used to be a wonderful antiquarian one in Railway Parade, Leederville and another in Nedlands where I have bought some of my old collectable books.
The other place to get fiction books apart from Op Shops, is at a swap meet. of which there are many on a Sunday morning.
I am a bit of a book hoarder and get most of my books from op shops rather than designated second hand book stores. There is a great one in the grounds of Shenton Park hospital run by Para Quad Industries. They have a large range of books that are reasonably priced.
I agree, Finy, that Elizabeth's is a great place to get secondhand books. In Bayswater, there are also a couple of places: there's a funny little shop in a side-street, not far from Bayswater Hotel, and another, more artsy one, next to the antique shop in King William Street. I'm sorry...I don't know their names or exact addresses.
Most op shops and flea markets also sell secondhand books, and you can sometimes find some real gems at these places....especially if you go op-shopping right out in the countryside.