another vote for Cambridge brewing - they don't have a large variety on at any one time, but if they have a barleywine on their barleywines are always very good
and another for Sunset Grill as a beer bar, you'll get to try stuff from almost every new england brewery you can think of
John Harvards in Harvard Sq. is good, it's a chain out here
Rock Bottom is good
Beer Works will probably be crowded with a Red Sox crowd while you're here



