Here is a list of useful links, mostly related to soccer around and outside of the San Francisco Bay Area.

Bay Area Adult Soccer Leagues and Organizations:

San Francisco Soccer Football League (SFSFL) - A men's league with several divisions in San Francisco comprised of teams from the bay area.  

Golden Gate Women's Soccer League (GGWSL)  - A competitive women's league with several divisions that plays games in San Francisco, the East Bay, and Marin.

San Francisco Recreational Co-ed  Soccer League (SFRCSL) - A 11v11 co-ed league based in San Francisco.  All games utilize a 5-touch rule (more than 5 consecutive touches =  foul).  All games usually played on turf fields.

Sports4Good - A bay area adult recreational sports league with several sports including a large selection of recreational soccer leagues.

NorCal Athletics - Norcal Athletics' mission is to provide a wide range of high quality sport and social events for the surrounding community (including a lot of soccer).

Golden Gate Sport and Social Club - Another organization of sports leagues, including soccer, in San Francisco.

San Francisco Soccer - A non-profit organization dedicated to promoting participation in recreational sports in San Francisco.

Bay Area Youth Soccer Leagues and Organizations:

San Francisco Vikings Youth Soccer League - A San Francisco recreational youth soccer league focused on fun.

San Francisco Police Activities League (PAL) -  They have leagues (including soccer) for youth with a recreational focus.

Mission Youth Soccer League (MYSL) - A part of the California Youth Soccer Association (CYSA), representing District 1 (San Francisco), this league has different levels of playing from recreational to competitive.

San Francisco Soccer Refereeing:

San Francisco Soccer Referee Association (SFSRA) - Servicing District 1 (San Francisco, Brisbane, South San Francisco, Daly City, and San Bruno) this website is a great place to find information for those curious or interested in becoming a referee.  United States Soccer Federation (USSF) sanctioned.

San Francisco Soccer Stores:

Sunset Soccer Supply - Great selection and owners who are very, very involved in the San Francisco soccer scene.  Two locations: One in the Sunset district of SF and a second in Marin near the Richmond Bridge.

Elite Sports - Also a great selection of gear.  Located in the Mission District of San Francisco.  Parking isn't easy to find, but public transport abounds in the Mission.