Lots of good suggestions for Boston already -- I'd just add:
1. Harvard Square in Cambridge. Very nice place, you can walk through Harvard Yard, and John Harvard's has some good house brews. If you're into pipe or cigar smoking, you should stop by Leavitt & Pierce, a great old-fashioned smoke shop. They also have a lot of nice knick-knacks.
2. Copley Square and nearby Newbury Street are really nice too. At the top of Newbury St. there's a bar/restaurant called Bukowski's too, which looks pretty cool on the inside. But Sunset has a better selection of beers, I think.
3. If you're into art, check out the Isabella Stewart Gardner Museum as well as the Museum of Fine Arts. They're right next to each other. The Gardner Museum is known for all the great art they've packed in to such a small museum as well as a fairly notorious art heist 10-20 (??) years ago. Several Rembrandts were stolen and never recovered.
Oh, and I'd personally skip the ICA. I went there in March, I think, and found it a complete waste of time and money. Extremely pretentious and self-loving place with mostly ridiculous modern "art" exhibits like videos of actual eyeballs on the floor, etc. One of their exhibits is a bunch of computers featuring video "exhibits" talking about how amazing the ICA is, how amazing the people involved are, etc.
