If you are going to San Francisco, then you should check out this really cool website. There are some really nice San Francisco vacation rentals there and they look they'd be the perfect place to stay so check this site out!
For places to stay in SF, I look to 'The Underground Guide to San Francisco'. The least expensive places it led me to are Europa at 310 Columbus & Golden Eagle Inn at 402 Broadway. Low costs & good locations (North Beach) keeps me coming back.