This isn’t meant to be comprehensive or list every shop in the area ... only the best.
If there isn’t a website, I listed a Chowhound report with the address. A newspaper article is the link if there were no Chowhound reports. Searching Chowhound will result in good tips for many of these shops.
I’ll update periodically with the suggestions in this topic noting additions with an edit comment at the end of this post.
I keep this list for my own info, so I don’t have to keep googling for websites. I would ask people NOT link to this in the future when questions about the best market, bakery, etc. are asked on the board.
Things change and it might discourage some great new hint. After a few days when a topic has run its course, then it's ok to link to this post as supplemental info, if anyone wants to.
*** Tops in its category IMNSHO (in my not so humble opinion)
BAKERIES AND BREAD
*** Acme (SF, Berkeley, various markets)
Arizmendi / Cheeseboard (SF, Berkeley, Emeryville, Oakland)
Bay Bread Boulangerie (SF)
Bread Garden (Oakland)
Emporio Rulli (SF & Marin)
Feel Good Bakery - Alameda
Golden Gate Bakery (pork buns, custard tarts) (SF) scroll waaay down
La Farine (Berkeley - morning buns)
Liguria (SF- focaccia)
*** Lola’s (Berkeley)
Masse's Pastries (Berkeley)
Sweet Adeline (Berkeley) http://www.imaginature.org/sweetadeli...
Tartine Bakery (SF)
Victoria Bakery (SF)
24th Street Cheese Co (SF) (scroll down)
Cowgirl Creamery’s Artisan Cheese Shop (SF) http://www.arizmendibakery.com/
*** The Cheese Board, (Berkeley) http://cheeseboardcollective.coop/His...
COFFEE AND TEA
Blue Bottle (SF, Berkeley)
Caffé Roma (SF)
*** Graffeo (SF)
Martha & Brothers Coffee (SF)http://www.marthabros.com/aboutus.html
Peet's Coffee (various locations)http://www.peets.com/default.asp
Far Leaves Tea (Berkeley, Emeryville
Imperial Tea (SF, Berkeley)
*** Teance (Albany)
Ten Ren Tea (SF)
This is not my area of expertise and I hope people will post about the well known shops. There are many markets and shops in the Mission, Chinatown, and Clement Street offering fresh meat, seafood and produce at rock bottom prices. Upper Geary has many Eastern European shops.
FARMERS MARKETS & FARMS
Berkeley Farmers Markets (Berkeley) http://www.ecologycenter.org/bfm/
*** Ferry Plaza (SF)
Old Oakland (Oakland) http://www.urbanvillageonline.com/old...
SF Civic Center (SF)
Other area farmers markets
A.G. Ferrari (various locations)
Genova Deli (Oakland) http://www.sfgate.com/cgi-bin/article...
Lucca Delicatessen (SF)
Molinari Delicatessen (SF)
Alameda Marketplace (Alameda)
Andronico's (various locations)
*** Berkeley Bowl (Berkeley) http://www.berkeleybowl.com/pages/mai...
Bi-Rite Market (SF)
Ferry Plaza Market Place
Mollie Stone's (various locations)
Natural Grocery Companies (Berkeley & El Cerrito)
Rainbow Grocery, (SF)
The Pasta Shope (Oakland, Berkeley)
Whole Foods (various locations)
MEAT AND SEAFOOD MARKETS
The above markets all have good meat and seafood departments. Check ethnic markets for inexpensive and fresh (even live) products. This article from the SF Chronicle discusses “building a repertoire with the local fishmonger”
The most farmers markets have fish and meat vendors. The Alemany market, for example, sells live chickens and you can buy a hundred small oysters from Pt Reyes Oyster for as little as $35. The Ferry Plaza Market has a number of top of the line meat vendors like Hoffman chickens and game birds. Many vendors, especially seafood, are dependant upon weather and season. They may not be there every week.
Barron's Meats (Alameda)
Bobby Lees Country Smokehouse
Bryan's (SF)` (and other butcher shops)
Café Rouge (Berkeley)
Ferry Plaza Merchants (SF)
Guerra Quality Meats (SF) http://www.sunsetbeacon.com/archives/...
Little City Market (SF) See Bryan’s link
Monterey Fish (Berkeley)
*** Tokyo Fish (Berkeley)
Ver Brugge Foods (Oakland ... see Bryan’s Link) http://www.rockridgeshop.com/pages/ve...
Scharffen Berger (various locations) http://www.scharffenberger.com/
Sees (various locatios)
*** XOX (SF, Oakland)
*** Note: Edited July 20 about 11 pm to include most of the shops mentioned up to that time. There are a few pending: Real Foods, Say Cheese, Cole Coffee and Village Market ... and who knew Monterey Market had a website ... good for them.