I recently got job offers from two companies, one in downtown San Francisco and one in the South Bay. I ended up going with the one in the South Bay because I couldn't figure out a way to commute into downtown SF in a timely manner. It seems that unless you want to live directly in the city, there's no way around a 40+ minute commute each way. By contrast I plan on finding an apartment within about a 20 minute drive to the office of the South Bay company.