After reading Jim's passionate lament on the passing of a favorite coffee shop, I had to chime in with a vote of extreme confidence for Flour Bakery.
Opened by a former pastry chef at Mistral and Rialto (I believe) Flour is fantastic. Great breakfasty breads, muffins, scones, and sandwiches as well. If you have to try just one thing to test my recommendation - make sure you get an oatmeal raisin cookie that has been out of the oven in the recent past. This could be the greatest cookie I have ever eaten.