Bukowski - beer bar on Dalton St between Hynes Convention Center and the Sheraton (but across the street). Closest T stop - Hynes Convention Center (green line). Great beer list. No idea if they serve food, but bring ID. They seem to card everyone, regardless of age and if you don`t have ID you have to leave.
Boston Beer Works - brew pub. One location across from Fenway Park and one near the Fleet Center. I`ve been going to BBW for about 10 years now, and love it, though I haven`t yet been to their "new" Fleet Center location. Closest T stop for the Fenway location is Kenmore (green line), the closest for the Fleet Center is North Station (green line).
Cornwall`s - beer bar. Kenmore Square (closest T stop is Kenmore (green line), exit the turnstiles, turn right, go up the stairs and it`s right there). Good tap list, including a couple of cask beers. Their old location across the street had more charm, but the new place is spiffier. They serve halfs, which I really like because I can try more varieties that way without getting sloshed.
Sunset Grill in Allston, mentioned by another poster, has a fabulous beer list, though they`re much farther out than either BBW or Bukowski. Not sure of the closest T stop, because I generally take the bus there (I live in Cambridge)
John Harvard`s - brew pub. Closest T stop Harvard Sq (red line). Good brews, good food. I think their beers in recent years have become a little boring, but that also might be because I go there too often.
Cambridge Common - beer bar. On Mass Ave between Harvard & Porter on the red line, closest stop probably Harvard. Good tap list, good rotation of beers, good turnover in kegs so brews are usually nice & fresh. Good pub fare.