There is a saying that death and taxes are the only real absolutes within the Human Experience.* In San Francisco, though, even death isn't a sure thing, or at least one's final resting spot can't be a certainty for...ever.**
At one time, there were probably more than 200,000 graves dug - some more than once - for each of the deceased residents in San Francisco before the year 1900. This was when the Board of Supervisors voted to stop all burials in The City and County of San Francisco, California. The exact number of the interred citizens within The City boundaries is hard to figure because most of the records were destroyed in the fires that resulted from the Great Earthquake of April 18, 1906.
Today, there are only two cemeteries, five columbariums, and one memorial (under the stones of a church terrace), inside The City limits. One cemetery is located at the Mission Dolores Church at 16'th and Dolores Streets. The other is The San Francisco National Cemetery/The Presidio, at the Old Presidio Army Base, which is now part of the National Park Service and the Golden Gate National Recreation Area. It is legally a seperate entity from San Francisco proper, but, from the earliest days it has always been considered a real part of The City .
The National Cemetery is still allowing a few select and special interments, like Philip Burton, as well as many various Honorable Military Veterans and their spouses.
The first columbarium, called the San Francisco Columbarium, is located at the end of Loraine Court, off Anza Street in the Richmond District and use to be part of the Odd Fellows Cemetery. It is run by the Neptune Society today and there are a few openings still available (They are going fast...) in the historic old building. An expansion or annex for offices has been built around part of the Columbarium and future work outside will allow more niches (Condos...as Emmitt Watson - Historian Caretaker - would say.) to be created.
The second columbarium is found inside of Grace Cathedral, on top of Nob Hill on California Street between Jones and Taylor Streets. The Grace Cathedral Columbarium is located in the Chapel of Saint Francis, on the second floor or level of the bell tower. There also are three additional columbariums located at St. Mary the Virgin, All Saints, and St. Gregory's Episcopal Churches. St. Francis Lutheran Church also places cremated remains under the stones of its Memorial Terrace. *+
There use to be numerous locations throughout The City where different religious groups and organizations bought land for the interment of their dearly departed members. There were Catholic,
Chinese, Jewish and Protestant Cemeteries as well as non-denominational and pauper plots covering many neighborhoods of San Francisco. Some say there were even Native American burials, like the site of the Old Spanish-Mexican Cemetery on the Main Post of the Presidio. I believe there are others as well, which we may not yet know about. There is also a charming Pet Cemetery near the Horse Stables in the Presidio today.
When the 1849 Gold Rush brought and overwhelming amount of people to San Francisco, land started to become a precious commodity. The early cemeteries, like the Yerba Buena Cemetery, which was located at the site of the old City Hall (first specifically built for that purpose) and is
now where the new Main Public Library has opened, were dug up and moved to various places farther west. As the population continued to grow, pressure continued to mount to remove all the "past" citizens from their "final resting spots".
For years the Richmond District cemeteries were 
neglected and vandalized. There was debate over what should be done. There were even four different years where Ballot Propositions and Ordinances were brought before the people (1914, 1924, 1925 and again finally in 1937) to settle the quandary over removing the cemeteries or just leaving them alone.
First there were a number of expulsions that began at the turn of the century and they continued again in the 1930's and 1940's until almost all cemeteries were eliminated within The City. Unclaimed headstones and monuments were recycled for building various seawalls, landfills and park gutters.
Basically, it is illegal to actually cremate anyone in town or bury anyone in the ground in San Francisco, California...proper. The only exception today is the San Francisco National Cemetery/The Presidio. The five Columbariums and the Memorial Terrace, of course, are for the interment of ashes only.
Many of the new cemeteries were created south of San Francisco in the town of Colma. Colma has the distinction of having more dead residents (around 5 million and counting) than living souls today. As a matter of fact, the cemeteries of Colma are considered some of the most beautiful in the World.
The wealthy barons from San Francisco's heydays built elaborate monuments to themselves which created a tourist destination which continues to this day.
The following is a list of the old cemetery sites around San Francisco, California.*** I have provided some information on each site and I have included some photos of some of the old sites as they appear today. I have also included some maps and articles about some of the cemeteries and related topics.