This list primarily includes what I know of or have read pretty clearly - there may be perfectly obvious things left out. Please let me know if you know of something that should be added.
At Stanford Mall in Palo Alto:
- Wilkes Bashford, selling L'Artisan Parfumeur and Penhaligon.
- Neiman Marcus.
- Diptyque boutique on Maiden Lane. (Very close to Union Square.)
- Hermes boutique on Maiden Lane.
- Chanel boutique on Maiden Lane.
- Barney's at 77 O'Farrell Street, near Union Square.
- Nieman Marcus at 150 Stockton Street, near Union Square.
- Gumps at 135 Post Street.
- Saks Fifth Avenue, 384 Post Street.
- Nordstrom at 865 Market Street.
- Fresh boutique, 301 Sutter Street. (And take a few steps and get some chocolate at Teuscher's, too.)
I've never been to these places, they're just mentioned in the Basenotes link above, some in rather old messages. Quite frankly, I'm putting them in here so that next time I'm in San Francisco, I can easily look at my own post and go have a look.
- Yves Saint Laurent boutique, Maiden Lane.
- Jaqueline Perfumery, 103 Geary Street.
- Kiehls, 2360 Fillmore Street and 865 Market Street.
- Wilkes Bashford, 375 Sutter Street.
- Yosh Olfactory Sense. I'm a little confused about the address, so I'm not going to risk giving it and being wrong.
- ElizabethW, 900 North Point Street, in Ghirardelli Square.
- In Fiore, 868 Post Street.
- Mahin & Co, 350 S. California Avenue, Palo Alto, is rumored to carry some L'Artisan Parfumerie, Bond No. 9, Caron, Different Company, and Jatamansi fragrances.
- Aftelier Perfumes, 1442A Walnut Street, #369, Berkeley. (Rumored. I don't know if this is a store that can be visited or just a company location that cannot.)
- Harmony Pharmacy & Health Center, San Francisco Airport. (Inside security. Been there. The selection of each fragrance was very limited, but I was still impressed.)
- Herringbone Apothecary, 1527 Shattuck Avenue, Berkeley. According to their website, they carry Mandy Aftel and CB I Hate Perfume fragrances. (Rumored.)
- Black Swan Boutique, 42 Elm Street, Los Gatos.
- Bliss Beauty, 682 Rancho Shopping Center, Los Altos. (Rumored.)
- A Basenotes post tells me that the Perfume Gallery in Valley Fair Mall, has a surprisingly good selection of classics. (Rumored.)
Edited to further clarify what's rumored and where I've actually been.
Photo of Union Square by Thomas Hawk. Wikimedia Commons.