Ask HN: YC Intern- Housing in San Francisco?

I am talking with one of the Y Combinator companies about interning this summer at their San Francisco office. I'm now looking for affordable living space in the San Francisco Bay area with transportation access to downtown San Francisco.

Does anyone have any suggestions on how to get the cheapest possible place within a reasonable distance of downtown besides Craigslist?

Are there any recommended modes of transportation to and from the city? Only one I am familiar with is BART.

Thanks for the help HN community!