A friend just wrote to ask me about sake pubs in SF, and after responding, I thought the information may interest others. Also, it would be nice to have responses from others to clarify, add to, or disagree with, my comments below.
** I don't know of any sake pubs, but there are eating places with pretty good selections.
1. Oyaji, a very Japanese style pub (izakaya) at 32nd and Clement, has a good selection, with great dishes to go with sake.
2. Sushi on North Beach, on Columbus, just up from Tower Records, which has a broad selection and a decently written menu.
3. Kiss on Laguna between Post and Geary. It's a sushi bar with izakaya-style dishes, and they have a nice selection of sake that is kept refrigerated after opening.
4. Memphis Minnie's on the 500 block of Haight, which is a pork BBQ place run by Bob Cantor, a guy who believes sake is the perfect match with barbecue. They offer a 3-sake sampler for just $8.
Also, there is also a place off Columbus in the upper stretch called Sake Lab, but I've never been there. From the outside it looks like a hyper-trendy bar, so they may not be serious anyway.
There is a sake retailer, True Sake on Hayes, which now has a particularly good nama-sake, Kamoizumi Shusen from Hiroshima, in a 900 ml bottle that is a particularly good value at about $26.