Have to chime in. I moved to the Bay Area for the cheap real estate, which everybody thinks I'm joking. Until I tell them its because we left Maui.
We selected Solano, which is about an hour fifteen or so outside of SF. But we selected it because we have friends in the area and like suburbia with walking distance to great schools, etc. So that was a factor for us. If not, I would have selected something closer to BART. That being said one of my friends who rents a room from me will be taking the Vallejo ferry into SF, as someone recommended, in order to keep his cheap rent (I'm charging a couple and with two dogs in my pretty spacious house for $500/month + utilities because I love them), but higher pay for commuting into the city. Its definitely do-able.
If you're going to take the job in SF try looking at all the BART communities. I work for Contra Costa County, and many of those communities are pretty swiss-cheesed in terms of nice vs cost. There are nice parts and not-so-nice parts of most of the places with a BART stop, the larger ones have more options like Concord whereas the smallest ones are kind of skewed one way or the other eg. Lafayette vs Antioch.
Its also partly a matter of what kind of lifestyle you want. If you want to be in the middle of things, if you go much further out than Berkeley you'll be commuting in for sporting and art events, which I'm okay with but others aren't. But I only go to plays and concerts once a month or so, not every weekend.
I can't help much with the idea of commuting to South Bay. My other roommate makes the haul to Fremont every day from here which I think is silly but he preferred living with and near friends to living with strangers. I will say that whenever possible, avoid driving, because the Bay Area has some pretty bad traffic these days.