If you go to Salem I would recommend the maritime NAtional Historic Site
http://www.nps.gov/sama/

I don't know whether you wandered around Beacon Hill in Boston during your first visit. It is not on the Freedom Trail so you may not have explored that area. It is worth exploring
http://www.beaconhillonline.com/cgi-bin/index.cgi

A fun quirky website with interesting Boston info is www.metaboston.com.

I recommend the new Institute of Contemporary Art in the seaport area (just take the redline subway to South Station and you can walk). You can walk from your hotel as well - head to the harbor and just walk south along the water. The Barking Crab is a fun restaurant right nearby.

I second Formaggio in Cambridge. The food is wonderful and if you are there on a saturday, there is usually a barbeque outside.

If you go to Harvard Sq. Sit out side at Legal seafood, tho a chain, the best seafood in Boston. Fresh, fresh.
Th Gardnr museum a must and is doible in a short time where the MFA, you need hours. The South end has lots of atmasphre and great rstaurants like Hamersley Bistro, Petite Robert.