Echo what zioxide said - check out the North End. After lunch/dinner Mike's Pastry on Hanover St. is awesome, and I should know, I used to work there in high school.

Just don't even think about bringing a car to the North End. The streets are 1700s tiny and there's never, ever parking. Walk over from Haymarket. Use the T in general where you can, there are tons of stops and it's convenient to all the major attractions.
Sam Adams tour is fun, and their Summer Ale is the truth. I really recommend having some good seafood while you're in Boston - particularly lobster (for which I'm drooling as I type this). Island Creek Oyster Bar is great (order the lobster roe noodles and die a heavenly, culinary-inspired death), as is James Hook & Co. Lobster isn't cheap, but New England seafood is worth it.
I'd also suggest checking out the public gardens, Boston Common, and taking a duck boat ride in the Charles River. It's a fun way to see a lot quickly.
If you're into shopping, Newbury Street is great, lots of boutique shops and some high end dining.
Don't do the damned accent! Many of us don't have it, and the Pahk the cah at Hahvard Yahd joke stopped being funny when it first started - i.e. it was never funny. Have fun and kiss Fenway for me.
