At the end of Fisherman's Wharf, near Ghirardelli Square, is the Buena Vista. The Buena Vista is the home of the Irish Coffee. This place was packed when we went in at about 8 o'clock. It was getting chilly out, so the coffee was warming me up (along with the alcohol). It looks like an old time diner/bar on the inside, and has a great view of the bay. I highly recommend heading here when in San Francisco.
Another place at the end of Fisherman's Wharf is Ghirardelli Square. There are shops here, but more importantly, the Ghirardelli factory. We got here late, but were able to go into the chocolate shop and try some chocolate. If I ever get back to San Francisco again, I will be getting here earlier and checking it out more.