Finding good coffee, despite the ubiquity of the word and its derivatives in many establishment names, is surprisingly difficult. As a rule, I don't go to chain coffee shops (read this to understand why; and if I do, I prefer Wawa and Dunkin Donuts over anything else). I like smaller places, where the focus is on coffee, roasting is done in house, baristas can paint latte art and tell you the region where the coffee is from.
The list below is not exhaustive by any means, but I have drunk coffee from each and every one of the places on it. My all time favorite coffee shops are Rojo's and Origo.