After getting some recommendations from some Harvard insiders, I checked out Daedalus a few weeks back and it was great. The roof deck is amazing for sunny afternoons and I'm sure i'll be back for the hot summer nights.
Charlie's is a hybrid bar/diner with a lot going for it. Head upstairs if you want more of a bar feel -- they've got more taps up there, TV's booths, and a more lively crowd. Downstairs is more about food -- which is not to say that it's bad. Good for late night drinks and eats.
During the summer months, they open up the patio and it's a great place to get cocktails. If you're not into the mix drinks, you can also waltz 50 yards away and get a beer at the Legal Seafoods outdoor bar.
With their addition of the outdoor beer garden, Charlie's gets my vote now. Awesome space with plenty of tables and good beer. The service is poor, but I'm willing to put up with it.
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