Rainbow Grocery - best bulk goods, organic groceries, cheese, and more (but no meat/fish)
Martin's Farm to Table CSA - best overall produce (on the adventurous side)
Frog Hollow Farms CSA - some of the best fruits (especially stone fruits) you'll find anywhere
Tara Firma Farms Meat CSA - best meat delivered to your door (especially pork, but also pasture-raised beef & chicken), plus you can get veggies & fruits
La Palma Mexicatessen - Mission District, best masa (corn flour), fresh tortillas, and other Mexican foods (like guacamole, queso fresco...)
Alemany Farmer's Market - Saturday mornings, best (and best deals for) fruits & veggies in town
...this is where we get most of our food, plus a smattering of stuff from "normal" grocery stores (like Costco, Whole Foods, and our local bodega-like neighborhood grocery stores)
...more details on each of these below:
SF Farmers' Markets (SFGate has a comprehensive list for the whole Bay Area; also see PCFMA's map/list and Cookhereandnow's SF list)
***Alemany - Sat dawn to dusk (but actually shuts down around 1 PM), 1000 Alemany (where 101 & 280 meet). One of the oldest in the area, and popular with foodies throughout the City.
Ferry Building - Tu/Th 10-2, Sat 8-2. The most "foofy" (high snobbery & prices) but also one of the best. Website and e-letter also include a guide to seasonal produce.
UN Plaza ("Heart of the City") - W 7-5:30, Sun 7-5, 1182 Market (@ 8th). Grimy part of town but great prices.
Inner Sunset - Sun 9-1, on 8th/9th Ave and Irving, fun neighborhood event...nearby at 840 Irving is Park's Market 2, a popular Korean supermarket known for good/cheap produce (M-Sat 9-7:30, Sun 9-7). Similar, further west, is the Greek-owned 22nd & Irving Market (not just produce but lots of Mediterranean stuff, M-Sat 7-6, Sun 7-5:30)
Upper Haight St - W 4-8, smallish but good
Noe Valley - Sat 8-1, 3861-24th St (@ Sanchez).
Fort Mason Center - Sun 9:30-1:30 Jun-Oct, Marina and Buchanan, nice views and easy parking
Crocker Galleria - Tu/Th 11-3, 50 Post (@ Montgomery), small market but convenient for folks who work downtown
Stonestown - Sun 9-1
Mountain View: Milk Pail Market - this parking lot market offers nice/gourmet stuff and fresh produce at (relatively) cheap prices...also see other produce chowhound rec's
Berkeley: Berkeley Bowl - highly recommended Berkeley institution with two locations that have great produce. For East Bay Farmers' Markets, see Rachel Trachten's great article.
San Francisco food purveyors:
***Rainbow Grocery - co-op grocery store with great prices and selection, awesome bulk goods (including a wide selection of herbs & coffees...Lizzie loves their Linea house decaf blend beans), cheese (the best cheese counter I've ever seen, including some fancy ones in France & Italy), natural herbs/supplements/skincare, etc...the only thing they don't see is meat/fish/poultry. Check their hours—in keeping with their progressive co-op nature, they tend to be closed on "leftist" holidays (like César Chávez Day and International Worker's Day) but not "nationalist" ones (like 4th of July).
Avendano's Meats - in Bernal Heights, one of the best places in SF, has a bunch of specialty stuff like guanciale (pork jowl, used for making classic Roman pasta dishes)
***La Palma Mexicatessen - near us on 24th Street in the Mission District, this neighborhood institution grinds its own masa (corn flour) and makes fresh tortillas every day (we love the organic blue corn ones, but all of them are great). They do pretty good tacos & other hot plates, and you can have a tasty but inexpensive party if you get their party plates and/or guisados (basically the filling for tacos). They also have great other Mexican foods (like guacamole, queso fresco...)
Limoncello - small chain that sells specialty Italian goods; they don't have the best selection of everything (e.g. they don't seem to carry pecorino romano) BUT they have great guanciale (I hesitate to say but better probably than Avendano's)
CSA (Community Supported Agriculture) Deliveries - organic local produce home (or "dropoff location") delivery
*** Martin's Farm to Table - Salinas farmer Martin Bournhonesque used to source veggies exclusively for Bay Area restaurants (including some high-end ones like Flour & Water and Delfina), but early in the COVID-19 pandemic he pivoted to allow ordinary folks to buy CSA farmboxes (and other treats from his & neighboring farms). His weekly emails often contain quirky, hand-wavy recipes and stories about unusual produce...definitely for people who aren't afraid of new things and who love high-quality produce.
*** Tara Firma Farms - not to be confused with "Terra" Firma, another local CSA, these folks in Sonoma County deliver excellent pasture-raised beef, pork, and chicken (among other things—their pork is especially good) in frozen bags to you on a regular schedule (weekly, every 2 weeks, every month, etc). You can also get a FEED Sonoma Bin and/or Fruit Share, which are both great deals with some tasty veggies/fruit.
***Frog Hollow Farms CSA - this organic farm in Brentwood (~1 hour east of SF) has amazing fruit, especially stone fruit; you can occasionally find it in grocery stores and farmer's markets, but their CSA offers first picks and great deals. During the winter, they partner with other farms to send you fresh citrus, etc. They also make some amazing fruit spreads (we especially like their apricot conserve, blood orange strawberry marmalade, and nectarine-plum conserve) and other goodies.
Others I've heard of: Farm Fresh To You (note not all their boxes are 100% local, but mostly from Capay Fruits & Vegetables), Two Small Farms (Mariquita and High Ground, probably one of the most "authentic"), Terra Firma Farms, Eatwell Farm (lets you choose more, so better for picky eaters) and Full Belly Farm. Also see Chronicle article.
Acme - This oddly named company (people think of Road Runner cartoons) makes some of the best bread in the area, including scrumptious baguettes, although their sourdough is not the traditional super-sour "San Francisco" variety. In addition to their main shop in Berkeley, they have a shop at the Ferry Building and you can find their bread (alas, not the "rustic" variety) at various other stores such as Whole Foods and Andronico's. The founder actually started making bread for Chez Panisse (see above).
***Tartine Bakery - 600 Guerrero @ 18th (Mission District). Foodies from all over the world make pilgrimages to get bread from this tiny bakery, which also features some great French-style pastries. Bread is available at 5 PM every day, but usually you have to call ahead (415-487-2600) to get a loaf.
Crepe & Brioche - great French-style bread, can't buy direct (they only do wholesale) but can buy at Avendano's Meats
#The Mill - 736 Divisadero (@ Fulton, Alamo Square), the appropriately named Josey Baker sells his bread here, as well as his (in?)famous $4 toast (and Four Barrel coffee)
Bay Bread (Le Boulange) - various locations, lots of good French-style breads and pastries
Boudin - classic San Francisco sourdough. Among their favorites is clam chowder in a bread bowl.
La Farine (?) - French style breads and pasteries
Fleur de Cocoa (Los Gatos...?)
Bordenave - in San Rafael, supposedly makes a good San Francisco-style sourdough?
Cheeseboard Collective - highly rated, crunchy baguettes, although apparently they only produce a small quantity each day and only sell from their Berkeley location...Arizmendi Bakery (1331-9th Ave) apparently uses many of the same recipes (?)
Bread Garden - a bakery in Berkeley, 19th Century baguette is highly rated
Chowhound's SF Board & Yelp SF - useful in many cities, and the Bay Area is no exception.
Bay Area Bites - nice KQED blog
SF Bay Guardian Best of the Bay - readers poll of restaurants, among other things; also worth checking out is SFGate's BayList.
KQED's Check, Please! - a show where 3 local residents talk about their favorite restaurants...and the other 2 visit to see if they agree
Eater SF - Interesting blog...includes their top 38 SF restaurants
San Francisco Grub Street (food news)
7x7 Magazine Eat & Drink - has a bunch of cool food-related lists/blogs/reviews, including 100 Things to Eat in SF Before You Die (updated 2012 list, with unofficial map)
Patricia Unterman's articles for the SF Examiner
SF Weekly Restaurant Reviews (mostly by Jonathan Kauffman)
The Bold Italic food stories such as Guide to Pop-Ups and Underground Supper Clubs
SF Chronicle food news/reviews, including Michael Bauer's blog, Top 100 Bay Area Restaurants (mostly upscale-ish Michelin-style)
Not for Tourists Guide - breaks down locally popular spots by neighborhood
Very impressive Foodie Google Spreadsheet - linked to a bunch of maps, includes info from 7x7 guides
Famousfood.us - lists famous places (from food TV shows, Michelin guide, etc.)