Well, if you are in town and do the Freedom Trail or Duck Tour thing during the day you could take in a play in the Theatre district in the evening.. Maybe hit one of the little cafe/resturants in the North End.
Cambridge (just across the river from the North End) has the Museum of Science as well as Harvard Univ. and MIT (and quite a few resturants in it's own right..).
The New England Aquarium is down on the waterfront (lotsa cute penguins!

) and they have Boston Harbor and Whale watching tours that launch from right beside the Aquarium.
The Freedom Trail covers most of the better known historical sites but there are some lesser know places too. The Union Oyster House where we had one of our A2K gatherings is the oldest tavern still in operation in the US.
If you do get out toward Concord/Lexington there is Walden Pond of Emerson fame as well as a replica of his cabin and a house that he lived in for a few years as a child.
If a car is available then a day trip down to the Cape Cod shoreline might not be to far fetched... (This really depends on which days you'd want to do it. Friday and Sunday trips to/from the Cape during the summer are just a bad idea from a traffic perspective...)