Fuck San Francisco. I was born there, lived there for 40 years. At some point I might have recovered from it to give some restaurant suggestions.
Honestly, the only place I really miss is R&G lounge, probably the most consistent and best Chinese in the city. Get the salt and pepper crab. Can't be beat. Most of the other good old places have gone away, leaving nothing but lines of sallow, skinny hipsters. God how I hate that place. There are other good Chinese places. The German is correct about the Chinese bakery, but how many egg custards can you eat? Z&Y Bistro is also very good Chinese. I am not Chinese, fwiw, but wtf, at least you find better food and fewer twats.
In all honesty, Tony's IS very good. It used to be the second best in town, but the better one moved back to NY. Otherwise, SF Italian food is pretty weak. I wouldn't touch the wharf with a ten foot dick. Sorry.
The food was honestly at its best in the late 90s, as was the rest of the city. It has become hollowed out in the same way without the residents noticing.
I dig La Taqueria in the Mission for tacos. Very good. My wife says that Californios, an upscale Mexican restaurant is really good, but I haven't been. All of the other high end places kind of blur into one. I can't say that any is better than the rest, just more pretentious and weirder. I guess if I wanted a really good meal in a nicer environment, I would suggest Delfina, but it is really hard to be around the people on that block, and I don't even think they shit the street.
Ranting aside, Cotogna is very good, as is Quince if you are looking to spend several hundred dollars a head. Kokkari has always been consistently good, especially the octopus appetizer and greek lamb. Can't go wrong with those.