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)
What are your top favorite bars in the Boston area?
The Middle East Cafe (Central)
Charlies (Harvard Square)
Plough & Stars (Central)
The Abbey Lounge (RIP)
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.