Forgive me, I know this subject has come up before, but as a bagel fan I wanted to give a few places in SF props. First of all, yes, yes, I know bagels typically suck rocks in SF: hard or too-soft lumpy bits that are simply baked or (heavens!) steamed instead of being boiled and then baked. I couldn't figure out when I moved out here why everyone had their bagels toasted - until I tasted them.
Two places that won't disappoint: Manhattan Bagels on Masonic at Haight (try the bialys and the everything bagel), and Sonoma Bagels at Sutter and Grant. Sonoma has some weird goyishe bagels such as chocolate chip, jalapeno and sundried tomato, urp. But they also have the perfectly-textured crust this transplanted eastener craves.