I was in SFO last week with a friend of mine, and we stayed at the Days Inn Civic Center. The hotel itself is nothing special, but the location is great and the price is right (I think we paid about $76/night? No crew rate, either). And when I say "nothing special" I mean B+ in cleanliness, pretty comfortable, and the front desk is closed overnight. For those on a budget, I'd absolutely recommend it.

My airline also has a special rate with the Hilton Garden Inn by the airport. They tend to fill up on weekdays, and it's a little (ok, a lot) further from the city center, but the price should be pretty decent if they are available to other airlines.