The SF Bay Area as a whole has some great holes in the wall, and there's even still some in San Francisco proper if you dig around, but in addition to being a bar in the Fairmont as others have noted, the Tonga Room is a world-famous tiki bar that opened in 1945, with two themed dining rooms that wrap around an artificial lagoon with a "rainstorm" every thirty minutes. That's a really weird definition of hole-in-the-wall. :)
While I haven't been up to SF proper for food and barhopping in a few years now, the Lark up in the financial district is much more of what I'd call a good cheap bar. I tend to bristle a bit at people dissing the SF food and drink scene, but I have to remind myself that with few exceptions my favorite places in the Bay Area aren't actually in SF itself. The metro area as a whole has virtually everything you can imagine at a very wide range of price points. I suspect one could make a case that the most interesting stuff happening is in the East Bay and South Bay, though.
While I haven't been up to SF proper for food and barhopping in a few years now, the Lark up in the financial district is much more of what I'd call a good cheap bar. I tend to bristle a bit at people dissing the SF food and drink scene, but I have to remind myself that with few exceptions my favorite places in the Bay Area aren't actually in SF itself. The metro area as a whole has virtually everything you can imagine at a very wide range of price points. I suspect one could make a case that the most interesting stuff happening is in the East Bay and South Bay, though.