I've mapped and annotated every public course in SF on the wiki... the link should be below in my signature.
My thoughts are Presidio is fun if you like uphill par 4s (8/10 play uphill). Do not play there after it rains as it tends to be the soggiest course in the city. The finishing hole at Presidio, I think, is the most beautiful finishing hole I've played in the area.
TPC Harding Park is a crucible. It is a course for people looking to test themselves. A word of caution, that tuesday/thursday they play the back 9 first and you will not feel the struggle of playing the long 18th when you're most exhausted.
Kevin is right that Gleneagles is an underrated architectural gem (full disclosure, I'm a member there), but if you care at all about high-end maintenance, it won't be for you. The greens are fine, but the club generally plays preferred lies because it can often be a crap shoot with the turf.
I'm more of a links guy, and I can't repeat enough how much I like the unfinished Corica: North Course just outside of town. To me it's the best course in the Bay Area, and a must for anyone who likes links golf, if you can play it on a windy day.
Just my thoughts.