mdmvrockford wrote: I second this recommendation of Linea. I've been to San Francisco at least 10 times but only truely tried and had palate to appreciate espsresso on last three trips. In general, the whole Bay area has TNTC great cafes.

+1 on Linea. My favorite espresso in SF

For those wanting to take a side track to Tartine Bakery, I recommend the Tartine Manufactory where they not only have their own coffee program, they offer the bakery, an ice cream bar, plus the Tartine Cafe. They are housed in the same building as the most excellent and interesting Heath Ceramic factory and outlet.
http://www.tartinemanufactory.com
http://www.heathceramics.com

Lots of great spots mentioned already! I'm gonna throw out a few more - but you'll be plenty busy even if you only tried to drink coffee!

If you're in the Mission (or out by the Presidio) Dynamo Donuts are great and they serve Four Barrel (and do a good job at it too).

Reveille Coffee Co / Cafe Reveille (depending on the location...) is great and have a good food selection.
Artis Coffee in Hayes Valley
Ritual Coffee (a few locations)
Equator Coffee (on Market a couple blocks towards Civic Center)
There's also a few in the North Bay (on the way to Napa) if you need a pit stop.
Cafe X - OK, this is a fully robotic machine in the Metreon a couple blocks from you. They serve AKA, Peet's and Verve and it's honestly pretty fun and a bit impressive to watch the machine. Not quite up to the level of a cafe, but a fun experience.