When I stay in SF, if I'm anywhere in the Mission, Castro, NoeValley, Western Addition, Lower Haight, Church St., Upper Market, or Upper SOMA districts - I walk over to Harvest Ranch around 9 to 10am for a delicious pump coffee with lots of soymilk and sucanat, and a loaf of freshly baked and just delivered Judy's Lovestick. Absolute carb head vegan heaven!!
For those of you unfamiliar with Judy's Lovestick, this is a vegan bread made in SanFran, and available at most area helth food stores. I can't even describe it, you have to experience it. Otherwise, Harvest Ranch Market is a basic independent health food store with a nice selection of veg/an alternatives for dairy, bread, meats, packaged foods, and some ethnic. Good produce selection, mainly organic, few veg/an toiletry items. Also has organic pet food. Prices may be a little higher than a lot of the big box type health food stores, but the local selection and community feel makeup for it. Great place to do light shopping or plan a meal but not a full grocery stop.
Cons: Has meat section.