Apartments for rent

Depending on what you're looking for, I would try craigslist.org. I'm not really an expert on real estate around the San Francisco bay area, but you might want to be careful for scams and stuff like that, but otherwise most of the advertisements that you see on the site are legit. If you want to read up on more of what the areas have to offer, try citysearch.

Here is the craigslist.org link: http://sfbay.craigslist.org/apa/

They usually have openings for people that are looking for apartments. Usually it's cheap because they expect you to split the costs with them. I have a friend looking for apartments in San Francisco as well because he's fresh out of college. I helped him look for an apartment on a nifty website: http://sanfrancisco.apartments.com/

This website might help with your needs as well. It gives ratings based on square feet, rent, and previous feedback from buyers and sellers.
http://www.apartmentratings.com/rate/CA-San-Francisco.html

Like I said, it's really your choice. Happy hunting!