SF's food scene is an embarrassment of riches. Do you know what area you'll be in for lunch or dinner? So many great places to eat in the Ferry Building alone--if you're early enough in the day, you can check out the large farmer's market there, as well as the many food shops inside.
My SF short list always includes Tartine (in the Mission), Cotogna and/or Quince (where we had our wedding dinner, the chef is a TU grad): LINK
And if you're into the touristy and downscale, there is an In-n-Out burger in the middle of the (completely skippable) Fisherman's Wharf area.