Before this year, OAK was the obvious choice. The airport was so much easier and the drive to the city faster. But lately the security lines at OAK are horrible, SFO has finished their huge construction projects and the train to the city goes right to the terminal. Taxis are VERY expensive and the train is cheap and easy.
The only major knock against SFO is the old runway configuration that causes significant delays when there are low clouds and fog, which happens quite often in that area. So if you absolutely have to be to a meeting in S.F. on-time, I would fly into OAK. But I might fly out of SFO since the lines are quicker and the train is easy. You can take public transportation to OAK, but it involves a bus transer.