Boston Duck Tours: Totally touristy, and also a total blast! We did the Duck Tour once when we were there in September, and it was so fun! Silly, yes. And it's hard to avoid the "Look at us tourists" deal when you're in a giant, "World War II amphibious landing vehicle." But yeah, completely worth it, especially at the beginning of a trip to get a feel for the layout of the city, and to note things you'd like to visit a bit more.
Boston Common: Boston Common was great to just wander around and chill out in. We spent hours here, just enjoying the feel of the area and hanging out.
Newbury & Boylston Streets: We walked along the posh shopping streets, and though we couldn't afford much, it was lots of fun to people watch and check out the awesome buildings along these two streets. We also went to Trinity Church and the Boston Public Library (AMAZING architecture) off of Boylston.
The Freedom Trail: 2.5 mile walk led by a red brick (or red paint) trail. It's a fantastic way to explore the history of Boston, plus it takes you through many of the places you would've wanted to see anyway: the USS Constitution, the Old North Church, Faneuil Hall, etc.
Paul Revere House: We visited the Paul Revere house when we did a self tour of the Freedom Trail. It was pretty cool for people who are into history!
Fenway Park: We were lucky enough to get tickets to a game at Fenway in 2005. I don't think we'll be able to do this on our next trip, but we will probably still do the Fenway tour!
Miss M and me at Fenway Park, 2005
The Boston Harborwalk
Sam Adams Brewery Tour
Isabella Stewart Gardner Museum
Something we looked into for our upcoming trip is the Boston Explorer Pass. You choose three attractions (one "premiere" and two "signature"), and then use the pass to save some time and money on the things you want to do. If we were to get one today, we'd get it with the following items: New England Aquarium, Isabella Stewart Gardner Museum, and Boston Harbor Cruises' USS Constitution Cruise. I doubt that we'll get them for this trip, since we'll only be in Boston for two days, but for a longer trip they would definitely be worth it.