Caffe Ladro may have made its reputation by siphoning business away from neighboring chain coffee joints (its name is colloquial Spanish for "coffee thief"), but has kept its clientele and built upon it by serving delicious fair-trade coffees with tasty baked goods. However, the old thief dies hard: Caffe Ladro snatched the win in this category from both Starbucks and Tully's.
You also mentioned...
Zoka, Java Bean, Diva Espresso, Bauhaus, Seattle's Best, Verité, Zeitgeist (Top Pot), Wonder Bar, La Vita e Bella, Torrefazione Italia and "my house at 5:30 a.m." We'll be right over.