The SF Legacy list, which lists San Francisco restaurants and bars around for at least 40 years http://chowhound.chow.com/topics/905397 , has tons of places more notable for their age than their food.
SF Eater compiled a list of what they consider the 25 most iconic "classic dishes" of SF, some not as old as the Legacy list, and you can use that to separate some of the wheat from the chaff.
What other specific dishes are worth seeking out at 40+ year old restaurants (change in ownership or not)? I'm a relative newcomer to the area, but some tips I've followed up on and enjoyed:
Art's Cafe (Bulgogi Hash Brown Sandwich) http://chowhound.chow.com/topics/922014
Boudin's dark bake (available at Geary & 10th by special order, or at Tadich Grill, Swan's Oyster Depot, Scoma's, and in a slightly lighter baguette form at Calabria Brothers http://chowhound.chow.com/topics/1002... )
Dianda’s Italian American Pastry : "chocolate mushroom"
Joe's Ice Cream : Joe's Its (higher quality proxy for It's Its)
La Palma Mexicatessen : hand-made tortillas, gorditas, huaraches, etc. from fresh masa (bagged tortillas use fresh masa that's been machine pressed, but still awesome)
Mario’s Bohemian Cigar Store Café : eggplant or meatball sandwich
Mee Mee Bakery : fortune cookies (samples at Golden Gate Fortune Cookie Factory's are always so overcooked I've never bought a bag)
New Woey Loy Goey : Cantonese Fried chicken and other delights http://chowhound.chow.com/topics/909754
Stella Bakery : sacripantina cake
Yasukochi's Sweet Stop : coffee, lemon, and chocolate crunch cake http://chowhound.chow.com/topics/31912