There are many free activities in San Francisco. 

Twin Peaks is a breathtaking view especially at night. 

In Golden Gate Park, the Japanese Tea Garden offers free admission the first and last hour of the day.  Next door at the DeYoung museum access to the 9th floor observation deck is admission free.  So too is the sculpture garden just outside of the cafe. The DeYoung offers a montly free day while  the California Academy of Sciences have a free day four times a year.  Check their websites for information.  The Conservatory of flowers, the Zoo, and most museums offer a monthly free day.  

City Guides offer many different  free guided walking tours of the city, check out their website for listings:  

If you have a rental car take the 49 mile scenic drive, the map is available from the visitors center.