We stayed at the Heartland Youth Hostel in Marin County (about 2 miles from the Golden Gate Bridge) and it was quite nice.  If you're a can-do person and don't mind making your bed and doing your own dishes, it's a great place to stay for $32 per day.   Bathrooms and kitchen are shared, plenty of room for all in the kitchen to cook your own food.  People on the whole are friendly although if you're stuck in a room with a person that snores like a grizzly bear you might find yourself sleeping in the common room.

GI Jaine...the only thing missing is the drill sergeant!  (Of course, Jaine's is the bottom bunk, and she may have to do fewer pushups for her bedmaking transgressions!)

The staff at the Point Bonita YMCA are awesome.  Jesse Wernick and Lara Hitchcock are very enthusiastic and extremely helpful people, you can see they are really into helping kids.  They were very generous with their time with us and would be really fun people just to hang out with.  A big thanks, Jesse and Lara!