We stayed one extra unexpected evening in San Fran at the end of our road trip. It was Saturday night and we were reaching the peak of our budget. For $30/person/night with world class views of the Golden Gate Bridge right outside, you can't beat it. This was probably the quietest hostel I have ever stayed in anywhere in the world (albeit not the cleanest, especially the showers). Sheets and towels are provided (they actually prohibit any outside bedding). Free parking!
Don't miss the Point Bonita Lighthouse at the end of the peninsula of the Marin Headlands. The 1 mile trip out offers spectacular views of the Golden Gate from several angles (the natural beauty of the surrounding cliff sides can't be beat either).
A SanFran must-do. $6 for a one-way ticket, exact change only. Hold on to your ticket stub, if you get caught riding without one you can be subject to a $75 fine. Don't miss the Cable Car Museum to really appreciate how the cars work.
The menu is generally overpriced and the service was so-so. But you MUST go for the sour-dough bread (maybe just skip the dine-in service). They've been using the same strain of yeast since they opened there doors!
Don't skip the Visitor's Center across the street. The visitor's center and exhibits are just as interesting as walking through the ships!