You could take a tour of the Freedom Trail.
Visist the USS Constitution, the Old North Church, the North End great Italian restaruants, take a walk in the Boston Common, visit Cheer's. Where ever you are staying ask the front desk if they have any ideas on historic places to see.
Hope that helps!! Have a great stay!

You mentioned the Smithsonian, if you are interested in museums, the Museum of Fine Art is world-class, and the Isabella Stewart Gardner Museum will take your breath away when you go in.

This is a big topic that is covered in just about any guidebook.  For me the unique features are:

- History. From the Freedom Trail that takes you to tons of Revolutionary War sites to Harvard Yard (the oldest University in America), Boston and Cambridge have tons of history.

- Neighborhoods.  The North End (very European - like a little bit of Italy), Charles St./Beacon Hill (old brownstone architecture, cobblestone streets, charming shops).  Newbury St.  Boutiques and chain stores, but people actually live there too.

- A walking city that isn't too big.  You can walk from Fenway Park, to Old North Church ("One if by land, two if by sea") in an afternoon, if you don't stop at the 1,000 interesting things to do along the way.  You can't do that in NYC or San Fran - those places are great but too big to see in a day or two.

- Universities and colleges.  Harvard, MIT, Boston U, Northeastern, Tufts, Boston College, Berkeley School of Music, New England Conservatory, Simmmons, Suffolk, Emerson, Emmanuel, UMass Boston - and those are just some of the ones within a 5 mile radius.  It gives the whole town a young feel and attitude.

- Unique local shopping areas, like Newbury St. or Charles St in Boston and Harvard Square in Cambridge.  While these have chain store as well, and aren't quite as unique as they used to be, there is still lots of local charm.  No need to go to a mall unless you just have to go to Dior or Ferragamo, and for that we have Copley Place.


filmat11

If you like museums check out the Museum of Fine Art or the Gardner Museum. The New England Aquarium is also a very popular attraction.

Just make sure you are not hoping to find a decent late night meal. Boston closes ridiculously early.

With regard to museums, I second the recommendations for the Museum of Fine Arts [www.mfa.org/] and The Gardner Museum [www.gardnermuseum.org], they both have exceptional collections.  For the best of what's current, try the tres mod Institute of Contemporary Art [www.icaboston.org/] with it's stunning harbor views (the most esoteric bartending in New England is nearby, at Drink [www.drinkfortpoint.com/]; no cocktail menu, you order the classics or just describe to them what you want).  Across the river in Cambridge, Harvard University has some fine museums as well: The Fogg Museum [http://www.harvardartmuseum.org/collection/fogg/], the Sackler Museum, [http://www.harvardartmuseum.org/collection/sackler/], the Semitic Museum [http://www.fas.harvard.edu/~semitic/] and the Harvard Museum of Natural History [http://www.hmnh.harvard.edu/] all have engaging exhibits.  Worth seeing in it's own right is the Carpenter Center for the Arts [www.ves.fas.harvard.edu/ccva.html], next door to the Fogg Museum, the only building in North America designed by Le Corbusier, and home of the Harvard Film Archive, with it's exceptional collection of celluloid and cozy cinema.  Also of architectural interest: the main branch of the Boston Public Library [http://www.bpl.org/central/] in Copley Square, with it's distinctive exhibits, fabulous collections, and it's gorgeous murals by John Singer Sargent, Edwin Austen Abbey and Pierre Puvis de Chavannes.  And if you have the inclination to venture a bit further afield, the DeCordova Museum [www.decordova.org] in Lincoln, whose Biennial [http://www.decordova.org/art/] opens on 01/23/10, or the Peabody Essex Museum [http://www.pem.org/]in Salem, which has one of the finest Chinese collections anywhere; the exquisite Yin Yu Tang house [http://www.pem.org/visit/yin_yu_tang.php], disassembled, shipped, and reconstructed in its entirety, is probably worth the price of admission.

to catch a show while we are here.  I saw it once at the Charles River Playhouse years ago.  Do they still do shows?

Have fun!

This is a college town and it is a hockey town. Head out to Boston College and watch two hometown rivals battle it out. BU vs. BC @ 7:30 tonight

Then for one of the most unique to Boston restaurants is Finale on the ground floor of the Park Plaza hotel. This restaurant only serves desserts. The most delectable and gorgeous desserts ever.

My two cents....