Bukowski's got one of the best beer slections in town. It's around the corner from Berklee, not far from the ball park. There is another bar over that way I like called TC's Lounge.

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I forgot to mention the Other Side Cafe if ur in the Berklee area. Corner of Mass ave and Newbury. Cheap pitchers and popular w/the bike crowd.
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Like jmberg mentioned, Central Sq is a must stop too. Lots of places to eat and drink.