Valencia Street Muscle = cheap and more free weights and barbells than any other gym I've seen. But is old school, broken and dirty. I guess thats what I love about it.
Embarcadero YMCA, also pretty cheap (compared to equinox and other alternatives in SF) and I go here to go swimming and play basketball and lift before heading to work. It's clean so the fiancee will go here (but not valencia st muscle.. where someone in nothing but a codpiece once worked out next to her)