Amoeba is by-far San Francisco's biggest and best known music store - and self-proclaimed "World's Largest Independent Record Store" :)
Be careful, don't buy more than you can carry... and try to save some new music for tomorrow, or the next day....
There are also many live (free!) in-store shows, usually in the evenings - check the calendar!
Address: 1855 Haight st, SF, CA
Website: http://www.amoeba.com/live-shows/calendars.html
Wikipedia: http://en.wikipedia.org/wiki/Amoeba_Music