For Berkeley, midday (anytime there are direct trains from SF, which is all day until about 630p or so), BART is the best bet, and if you are more than a short walk from the 3 Berkeley BART stations, get a cab at the station. OW fare is about $3.50. I wouldn't even consider a cab the whole way. For Stanford and SJ, I'd rent a car. Your other alternative is Caltrain, and then get a cab from the station(s).