Consider Gleneagles. Here is what the course website says...
"Best public golf course in San Francisco" -- S.F. Weekly "2007 Best of San Francisco"
"Built in 1962, Gleneagles GC in McLaren Park is a challenging course that has quietly become one of San Francisco's purest golf experiences. Located at the far southern point of The City, Gleneagles GC is home to tough topography, slick greens, and one of the finest 19th holes in all the golf kingdom.
"Choose to discover this piece of local links history, and you'll be on your way to a cherished golf course. There aren't any big signs, fairways visible from neighboring streets, or hype of any kind. Just a hard player's course, that's been home to everyone from City mayors, low digit players, and a loyal crew of golfers who only speak of it in whisper.
"Nine regulation holes with 18 different tee boxes are enough to test the mettle of the shrewdest shot maker. The sprawling bay vistas, Cypress lined fairways, and fast greens have hooked a devoted following who keep a watchful eye on newcomers for fast play and religious repairing of divots and ball marks."
I played there a number of times in the late 1980's. Thoroughly enjoyed the course. Hear it's in better shape now, too. Maybe some locals can comment.
One other advantage of Gleneagles: according to the website, 18 holes costs just $23 Money thru Thursday.