The Modern Pastry thread got me to thinking of my favorite bakery, which I don't recall ever having been mentioned here before:
1373 Massachusetts Avenue, Arlington
(I think this is considered Arlington Heights? It's several miles past the center of town headed West). They bake nothing but cookies, but they are the best cookies you will ever have, well worth the drive. You can find their cookies as Rancatore's ice cream shop in Belmont and Darwin's in Harvard Sq. as wel.