I have an affinity with coffee beans, recording (in my head) what shop carries what. I often ask or chat the nice baristas about it. Also enhances my coffee experience. Anyhow, stopped by a San Francisco favorite recently. Farley's Coffee was my lifesaver during school, when not too many shops back then opened later than 8pm (they open til 10pm)
For a long time, they carried local Mr.Espresso beans but, have recently made the switch to (also local) Sunrise Coffee. ‹more info from their site here›
Other than that (and making an appearance in that one movie, Sweet November (see the scenes -scroll halfway to here), they have the best city skyline view out of Potrero Hill. Good stuff.