You can't possibly be in San Francisco for that long and not eat at:

#1: Swan Oyster Depot (polk/california) – Always my first stop for lunch, usually straight from the airport. Anchor Steam (while waiting in line), cup of clam chowder, fresh bread and butter, 1/2 dozen mixed oysters, prawn and crab louis salad. Grab a free chocolate sample at the See's Candies next door to top it all off. Family run for at least 50 years, probably longer – introduce yourself to one of the brothers and they will greet you by name the next time that you visit, even if it's not for another 6 months to a year. In my opinion, the #1 absolute best lunch place in the entire country.

#2: Atami Sushi (lombard/octavia) – The best sushi restaurant in SF run by a staff of three people every night that it is open. Wiley (former chef at Ebisu (also great for different reasons, mostly the #29 roll and Tommy, who is still going strong – hai! )), Michelle the waitress and a single bus-boy – they do everything. The sushi is relatively small, expensive, served in a very simple, unassuming atmosphere and worth every penny. Try everything, it's all great.

Lots more recs if you like those two…