Well, if we're talking straight up bars, and not pubs/restaurants, then:
Brendan Behan
Bukowskis
Deep Ellum and Sunset are great, but they feel like restaurants that serve good alcohol, and not primarily bars (or even pubs for that matter).
Btw, I don't think Plough and Stars is a dive and I don't think The Middle East is one either - plus it's not a bar, it's a restaurant/club which serves drinks.
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Wow, that reads a lot more negative than I intended - perhaps I better relax and have a homebrew!
Lots have been missing the love! I'm probably prejudice to where I live of course, but in addition to the awesome bars already mentioned:
-Lord Hobo (I know this was already mentioned but it deserves another bump)
-Russell House Tavern in Harvard Square (also a restaurant but great place)
-John Harvards brew house (I like the basement-vibe and always some decent beer at decent prices)
-Plough and Stars (especially on live music nights)
-Cambridge Brewing Co (wish I could get there more)
I would have to say that I like Charlie's and Eastern Standard. They are on both sides of the spectrum, but great places for just grabbing a beer or trying a really unique cocktail, respectively.
What are your top favorite bars in the Boston area?
Mine:
McGreevy's
The Middle East Cafe (Central)
Charlies (Harvard Square)
Plough & Stars (Central)
The Abbey Lounge (RIP)
The Model
Bukowski's
Yes, I like the dives!
Even though it is a complete dive, I love Sully's Tap near the Garden. I go there before every Bruins/Celtics game I attend. Al and Matt are great bartenders and hilarious to joke around with. Oh, but stick to bottled beers in there. Some of the tap lines must not be cleaned very often.
Can't believe Doyle's hasn't been mentioned, just for the history of the place. Also, The Behan, Sunset, Publick House, Deep Ellum, but they've been mentioned.