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Whiskey Bar for upscale lounge. B Side Lounge for low key drinks. Beacon Hill pub for getting very very drunk. I like Limbo to watch jazz and I like Harvard Gardens for a normal bar.
Not to be rendundant, but I have to say that everything Tim wrote is dead on (except the Whiskey Park crowd is a little skeezy--lots of meatheads and wanna-bes.)
Franklin Cafe and Tremont 647 because they are in the South End, Last Drop in Back Bay and Sevens in Beacon hill because they are what a neighborhood bar should be.