If you want a fun tour, consider "duck tour".
If you like to walk, here is a standard walk I take the visitors on in Boston:
1. Take the green line T to "Hynes Convention Center".
2. Walk over to Newbury Street. Walk all the way through Newbury Street to Public Garden.
3. Cross over Boston Common
4. Make a left on Charles street to get to Beacon Hill. After crossing Beacon Street, walk another couple of blocks to Mt. Vernon St. and make a right. Walk the whole length of Mt. Vernon. This will give you a good sense of Beacon Hill (including Lousbourg Square which you will pass on your left).
5. At the end of Mt. Vernon, make a right and another right. Admire the State House.
6. Walk across Boston Common to Tremont Street.
7. Take any of the streets (I suggest Winter St) to Washington St. Make a left on Washington. This will give you a good sense of Downtown Crossing.
8. Take Washington all the way to the end. Make a right, then left on Congress. Walk over to Fanueil Hall (if you want to, walk a little further to see the Holocaust Memorial).
9. Walk across the Fanuiel Hall/ Quincy market. It's very touristy, but fun.
10. Walk across to Christopher Columbus park on the waterfront.
11. From here you have two options. One is to make a right on Atlantic Ave, and see Long warf, Roes ward, etc. If you want a harbor cruise, that's where you start. Also, the boston aquarium is there.
12. The other option is to take a left on Atlantic, and cut across any of the streets to Hanover. This takes you to North End, Boston's rather authentic Little Italy.
In addition to this "tour" of mine, there is the must see of Harvard Square in Cambridge. There are also some historical sites that I frankly don't find particularly interesting. If you have time, also see the South End - following its gentrification, it's the true gem of Boston. Also, walk at least a few blocks of Commonwealth Ave in Back Bay - you really get the sense of the area. There is also the Chinatown. If you want a good arial (sp?) view of Boston, a cup of coffee at the "Top of the Hub" - restaurant at the top of the Prudential; the view is amazing.
If you have to take 1 guide book with you, I highly recommend
the Rough Guide to Boston. It doesn't just tell you the obvious; it really hits the out-of-the way spots, such as the Japanese Mall where you can have the best (and among the cheapest) sushi around.