San Francisco Bay Area is one of the most diverse and best areas in the United States (perhaps the world?) to find bookstores for special audiences (eg: non-English language and Sheet music) and for independent bookstores.

Independent Bookstores 

The independent bookstore is practically becoming an endangered species in the United States. Many have closed, the victims of chains and internet bookselling. But in the San Francisco Bay Area, especially in San Francisco and Berkeley, a glorious array of independent bookstores live on. If you're a book-lover and coming to San Francisco, check some of these out.

Alexander Book Company--50 Second St (near Market St.)., San Francisco: A fine general and literary bookstore in the San Francisco Financial District, with a special emphasis on books by and about African-Americans. Open weekdays only, because that's when the Financial District is. Transit: Montgomery BART and Muni Metro. Near California Historical Society, Foto-Grafix Books SFMOMA.

Argonaut Book Shop -- 786 Sutter St. (near Mason Street) San Francisco: Family-owned rare book shop, specializing in the Gold Rush era and early California. Widely believed to be the inspiration for the Argosy Bookstore in Alfred Hitchcock's classic, "Vertigo," which was takes place in San Francisco. Hitchock spent time in the Bay Area on weekends. The Argonaut's owner says his father, Robert Haines Sr., who founded the store on Kearny Street, knew Hitchcock and was the director's model for the Pop Leibel character.

Black Oak Books--1491 Shattuck Ave (at Vine)., Berkeley: A big, wide-ranging mostly used bookstore, with a good selection of new books in Berkeley's "Gourmet Ghetto." Particularly strong on fiction, politics. Transit: About 15 minutes' walk to Berkeley BART; AC 7, 9, 43 buses

The Book Smith -- Haight-Ashbury District store. Awaiting contribution here.

City Lights Books--261 Columbus Ave (at Broadway), San Francisco--North Beach's great bookstore of the Beat era lives on, as vital as ever, and Lawrence Ferlinghetti is around too. Literally floors of poetry you won't find anywhere else, and a whole basement full of world history, politics, geography. Some creatively named sections. Transit: Muni 15 Third St. or 30 Stockton.

Cody's -- 1730 Fourth Street, Berkeley -- Cody's last, remaining location, but in an inviting one: Berkeley's new bustling "gourmet ghetto" district. This location is meant for browsing. There's a Peet's Coffee just steps away and more people kicking back in the sun-drenched sidewalks than you thought possible on a weekday. And this location, too, hosts a calendar of authors. Betty's Oceanview Diner, and more.  Cody's gamble on Union Square failed in 2007, and its flagship store on Telegraph Avenue closed earlier, R. I.P. for a great independent book store.

Dark Carnival--3066 Claremont Ave (near The Uplands)., Berkeley: One of two science fiction bookstores (the other being Another Change of Hobbit in Downtown Berkeley). Dark Carnival also has a strong selection of mysteries on its shelves that seem to stretch back forever . Sometimes strange--the books, the store, the staff--but good. Transit: AC Transit 7 to Rockridge BART. Near Afikomen

Eastwind Books of Berkeley-- 2066 University Ave (near Shattuck)., Berkeley: Downtown  Berkeley's Eastwind still specializes in books about China and Chinese America. Transit: Berkeley BART

Eastwind Books San Francisco -- 1435 Stockton St (bet. Vallejo and Green streets), (415) 772-58771435 Stockton St, (415. 772.5877) The Chinatown location of Eastwind features everything from books to magazines to greeting cards. Extensive collection of Asian American works, with a focus on Chinese, and Chinese-American, in particular.

Forest Books--3080 16th St. (near Valencia) St., San Francisco--There's a collection of mostly used bookstores along Valencia St. from 16th St. to 20th St. in San Francisco's renowned hipster/Latino Mission District. Forest Books has one of the most careful selections, particularly strong on literary titles. Transit: 16th St. Mission BART; Muni 14 Mission, 22 Fillmore, 26 Valencia. Near Modern Times.

Green Apple Books--506 Clement St. (near 6th Ave.), San Francisco--Out in San Francisco's foggy (and foodie) Richmond district, Green Apple Books is one of the largest used bookstores (with some new books) around. Transit: Muni 38 Geary, 1 Caifornia, 2 Clement

History books--California Historical Society--678 Mission St. (near 3rd St.), San Francisco--There's a small but intriguing California history  bookstore  tucked into a corner of the California Historical Society's galleries in Downtown San Francisco. Open limited hours. Transit: Montgomery BART/Muni Metro. Near Alexander Book Company, Foto Grafixd Books,  San Francisco Museum of Modern Art.

Israel books--Afikomen--3042 Claremont Ave (near The Uplands)., Berkeley--Afikomen somewhat alarmingly describes itself as "your Jewish lifestyle store"--it's the place for all subjects Jewish in English or Hebrew. Transit: AC 7 to Rockridge BART. Near Dark Carnival.

Japan books-Kinokuniya Books--1581 Webster St (at Post St.)., San Francisco--This bookstore in the Japan Center mall makes a credible claim that it has the biggest selection of books about Japan in the United States. English and Japanese. Transit: Muni 38, 2, 3, 4.

Kayo Books--814 Post St. (near Leavenworth), San Francisco--This quality used bookstore west of Union Square describes its stock as "pulp and vintage popular culture," the stuff you used to have read sneakily. A favorite of John Waters. Transit: Muni 38, 2, 3, 4

Lewin's Metaphysical Books--2644 Ashby Ave. (near College Ave.)--Lewin's had a fire some years back and  the owner was quoted as saying that first he was upset, then he realized material things weren't important. Then he rebuilt. A man in tune with his books. Transit: AC Transit 51 to Rockridge BART or Berkeley BART, AC Transit 9

Marcus Books -- 1712 Fillmore Street, San Francisco (415.346.4222) : That's Marcus, as in Garvey. Dedicated to the education, history and future of African Americans. Everything from children's books to biographies and academic texts.

Marcus Books - 3900 Martin Luther King Jr. Way, Oakland, CA, (510.652.2344): This is the original store, and the place to come for books from the African American pont of view.

Moe's Books - 2476 Telegraph Ave., Berkeley, CA 94704-2392  (510. 849.2087): for a booklover, any trip to Telegraph Avenue had to include several hours at Moe's and Cody's. Now only Moe's is left. What are you waiting for? BART to the Berkeley station, then walk several blocks to Telegraph Ave. 
 

Modern Times-- 888 Valencia St. (near 20th St.)--Modern Times describes itself as a "progressive resource" and it is, with politically concious books (of no single persuasion) ranging  from sociology to sexuality. Transit: Muni 14, 26. Near Forest Books

Oakland Museum Bookstore-1000 Oak St. (at 10th St.), Oakland--The Oakland Museum of California art, ecology, and history and is an underappreciated treasure, and so is its bookstore on these topics. No entrance fee. Transit: Lake Merritt BART

Photography Books-Foto-Grafix Bookstore--655 Mission St., San Francisco--The Ansel Adams Society had to give up its gallery  in high rent Downtown San Francisco, but it left behind this comprehensive photography bookstore. Transit: Montgomery BART/Muni Metro. Near Alexander Book Company, San Francisco Museum of Modern Art.

"Queer" Books--A Different Light--489 Castro St. (near 18th St.)--A large  gay bookstore in the heart of The Castro  that also has outposts in Greenwich Village and West Hollywood. Stock goes from serious to sin-filled. Transit: Castro Muni Metro, Muni F, 24.

San Francisco Museum of Modern Art Bookstore--151 Third St. (near Mission)--The San Francisco Museum of Modern Art is famous (or infamous) for having turned its bookstore/gift shop into a massive profit center. A good place to look for art books and related topics,  not just on MOMA's exhibitions. Transit: Montgomery BART/Muni Metro. Near Alexander Book Company, California Histrocial Society

Travel books--Get Lost--1825 Market St. (near Octavia), San Francisco--The travel bookstore seems to be disappearing from the scene but Get Lost will still help you with books and accessories  if you have the incomprehensible desire to go somewhere besides San Francisco.  Transit: Church St. Muni Metro, Muni F streetcar

University Press Books--2430 Bancroft Way (near Telegraph Ave.), Berkeley--Across from the University of California Berkeley campus, this bookstore specializes in the scholary and sometimes obscure publications of university affiliated presses. Transit: Berkeley BART (@15 minutes walk) or AC Transit 51, 40, 7. More bookstores--Cody's, Moe's, Shakespeare's--three blocks south on Telegraph Ave.

William Stout Books--804 Montgomery St (near Jackson), San Francisco--William Stout tried a branch on trendy South Park, just as the dot com boom busted. Now its back in its main Jackson Square store, feature big, beautiful (sometimes really expensive) architecture, design, and urban planning books from around the world. Transit: Montgomery BART (@15 minutes walk), Muni 15, 10

Zen Center Books--300 Page St. (near Laguna St.)--What is the sound of one page clapping? Transit: Muni 6, 7, 71.