I always recommend starting your online search at SF Genealogy, the outstanding resource for all things San Francisco genealogy related.
But below is a list of resources available at the two biggies - ancestry.com and FamilySearch.
Please note that these lists are accurate as of December, 2013 and may change after this date.
Yes ancestry is a subscription based site, but if you have access to a subscription - don't miss these resources. The list is presented in order of size of collection:
- California, Voter Registers, 1866-1898
- California, San Francisco Area Funeral Home Records, 1895-1985
- San Francisco, California, Chinese Applications for Admission, 1903-1947
- U.S., Registers of Chinese Laborers Returning to the U.S. through San Francisco, California, 1882-1888
- U.S., Chinese Immigration Case Files, 1883-1924
- San Francisco Chinese Exclusion List
- San Francisco, California, Immigration Office Minutes, 1899-1910
- Alcatraz, California, U.S. Penitentiary, Prisoner Index, 1934-1963
- The history of San Francisco
- The Bay of San Francisco : the metropolis of the Pacific Coast and its suburban cities : a history.
- Benjamin F. Taylor, Trip to San Francisco, 1870s
- The annals of San Francisco : containing a summary of the history of the first discovery, settlement, progress and present cond
- Clifford Allen, Rail Trip to California, early 1900s
- San Francisco : the bay and its cities
- Albert Williams, San Francisco, California Pastorate, 1849-54
- Lights and shades in San Francisco
- William Chambliss, San Francisco Society, 1895
- San Francisco : a pageant
- San Francisco Ship Passenger Lists. Vol. III: November 7, 1851 to June 17, 1852
- Inventory of the county archives of California: The city and county of San Francisco.
- San Francisco Ship Passenger Lists Vol. II [1850-1851]
- Complete story of San Francisco's terrible calamity of earthquake and fire : the most appalling disaster of modern times : imm
- San Francisco Ship Passenger Lists Vol. I [1850-1864]
- Villains and vigilantes : the story of James King of William, and pioneer justice in California
FamilySearch is a free resource and there is tons of information available in these online records. Not all collections are indexed so you may need to browse through some of them, but try browsing. I have found lots of documents while browsing.
- California, Birth Index, 1905-1995
- California, Births and Christenings, 1812-1988
- California, Cemetery Transcriptions, 1850-1960
- California, Collections of the California Genealogical Society, 1700-1942
- California, County Birth and Death Records, 1849-1994
- California, County Marriages, 1850-1952
- California, Death Index, 1905-1939
- California, Death Index, 1940-1997
- California, Divorce Index, 1966-1984
- California, Great Registers, 1866-1910
- California, Marriage Index, 1960-1985
- California, Marriages, 1850-1945
- California, Northern U.S. District Court Naturalization Index, 1852-1989
- California, Probate Estate Files,1833-1991
- California, San Francisco Area Funeral Home Records, 1835-1931
- California, San Francisco County Records, 1824-1997
- California, San Francisco Passenger Lists, 1893-1953
- California, San Francisco, World War I Enemy Alien Registration Affidavits, 1918
- California, San Mateo County Records, 1851-1991
- California, San Mateo County, Colma, Italian Cemetery Records, 1899-2011
- California, State Census, 1852
Good Luck and Happy Hunting!