I went there in 2008 for a work trip, so my knowledge is a bit old. Get on the Trolley Tour and it will take you most of the places you might want to see. Museums, the aquarium, Faneuil Hall and the Quincy Market, the Bunker Hill Monument, USS Cassin Young and USS Constitution, Boston Common, Old State House, the Paul Revere House and Old North Church, Copps Hill burial ground, Charles River Esplanade, the Freedom Trail, Cheers, Fenway Park. Cambridge. Nearby is Salem. You won't have the problem I did; October 30 is a bad day to visit Salem. Crowded and all the nuts were out in force! I went with friends from work. It was hilarious -- Michael and I trying to find our way back to the van with duelling GPS devices while Linda and Laurie were waiting. If you stop by Salem, skip the Witch History and Pirate Museums. Totally boring and filled with truly creepy mannequins. Take extra time if you want to get into the House of the Seven Gables.
My pictures are with an old Pentax Optio and not the greatest (my coworkers tolerated my camera habit,) but if you're interested, check out my Flickr sets:
Boston Salem