The best bread I've had in the US is at
Acme which started in Berkeley but is also in the Ferry Building market. Berkeley also has terrific chaat at
Vik's, which is basically a barebones warehouse operation adjacent to their food import business.
In the Castro is Anchor Oyster Bar, which has the best New England clam chowder I've had. It's a little neighborhood secret with the same guy in the kitchen every day.
The standard touristy (yet still very good) Chinese place is House of Nanking but down the block and up Broadway is Yuet Lee, which IMO is much more delicious. I'll typically just order whatever specials they have and go to town.
Another tradition was having a sausage foccacia sandwich and some good coffee at Mario's Bohemian Cigar Shop off Washington Square or getting a delicious sandwich at Molinari's, a couple blocks down Columbus. Molinari also makes fresh ravioli that you can buy by the box.
EDIT: Forgot about
Pyung Chang in Oakland. Excellent soon dubu for people who like Korean food. And
Avatar's Punjabi Burritos in Mill Valley.