We were there in Aug 2008 and took the Old Town Trolley tours...
http://www.trolleytours.com/boston/
It is a bit pricey, but worth it, IMO. You can get off and on the trolley throughout the day at your pace. We only had time to use it one day due to time constraints, but there is a 2-day pass that makes it more economical. We were able to see most everything in one day, but two days would have been very nice to have.
We go out there every 2-3 years and we never run out of things to see. We already have a list for next time - go back to the Museum of Science and possibly the Salem Witch Museum. In years past the witch museum would have held no interest to us, but in doing my husband's genealogy we have found one of his ancestors involved in the trials.
Over the years, we have enjoyed ....
The Swan Boats ....
http://www.swanboats.com/
Mike's Pastry in the North End ...
http://www.mikespastry.com/index.html
Fenway Park Tour ....
http://boston.redsox.mlb.com/bos/ballpark/tour.jsp
Shopping/Eating at Fanueil Hall ....
http://www.faneuilhallmarketplace.com/?q=shoppingdining
also the Old North Church, several historical cemetaries, Paul Revere's house, The Freedom Trial and the USS Constitution.
...and though you can't say it was something to be enjoyed per se, the New England Holocaust Memorial was very moving and most definitely something to see and experience ...
http://www.nehm.org/
We spend most of our time in MA outside of the city, but it is always fun to go into the city to explore too.
Have fun!!