If you get up north at all, Grant's Pipe Shop in the city isn't too bad. A few blocks away is The Humidor and they sometimes stock some decent tins. There is a cigar bar in the city, can't remember the name off the top of my head, but they allow smoking and are apparently cool with pipes and cigars. My favorite shop in the area is Telford's, but they're up in Mill Valley, north of the Golden Gate Bridge.