My SF rec copy pasta. I can make a list for the South Bay too... (San Jose and its surrounding suburbs). It skips a lot of the really famous spots like Fleur de Lys, Gary Danko (kinda overrated), etc.
If you're not leaving the actual city:
Coffee - Philz, Sightglass if you're a snob
Snacks/between meal stops - Swan Oyster Depot, SOMA StrEAT food park (food trucks/microbrews on tap), show dogs
Burgers - a lot of places in SF make good burgers - B Bar (Yerba Buena garden...