-If you like history, there are many historical sites, most of these located along the Freedom trail.
http://thefreedomtrail.org/
-If you like art, there are the Museum of Fine Arts (large museum) and the Isabella Stewart Gardner Museum, both of which have wonderful collections. There are also galleries along Newbury Street, many of which are open to the public.
-There are a bunch of plays showing in the theater district.
-The North End has many good Italian restaurants, though the food is pricey. Mike's Pastries is a popular destination there; their desserts are pretty good.
-I believe all of the Cheers bars are regarded as tourist traps. I don't know the various bars around Boston well, but my family likes Boston Beer Works, which is just across from Fenway Park.
-If you don't want to spend money, I'd recommend just taking a stroll along the Charles River on a nice day.

My advice is to train. I hear these marathons are pretty long.

The Esplanade is great. Similar to the lake front in Chicago, or so I've been told. I'm sure your training regimen is worked out, but if you're going for a run, the Esplanade is the place to do it. Take the T to the Museum of Science, run along the Boston side, cross one of the four or five bridges to Cambridge, and run back. Great views.

The North End is awesome. Cobblestone streets, canolis, Paul Revere's house, the Old North Church ("one if by land, two if by sea"). And if you like pizza, I think the original Pizzeria Regina's is the best in the world. Yes, I've had Chicago pie, and I currently live in NYC, but Regina's IS pizza to me. The waitresses are rude, and the place is small, but it's got character. I'd recommend getting off the T at Haymarket, walking through Fanueil Hall and Quincy Market, and crossing over the Big Dig "Green way" to Hanover or Salem Street in the North End.

Beacon Hill is cool too. Cobblestone, food, brick townhouses, John Kerry.

Avoid Cheers. If need be, on the way home, hit the one at Logan with the mechanical Norm and Cliff. The coolest bar I've been to recently is the Liberty Hotel. It's an old prison from the mid-19th century that had been abandoned and had fallen into disrepair, they renovated it and turned it into a big hotel with a couple cool bars. It's a little trendy for my tastes, but it's still a cool space. You could even check it out during the day - the main room has the original dome from the prison.

Newbury Street is all right. A bit spendy, but it's fun for people watching, and as was said above, the Galleries are nice.

The Museum of Fine Arts is great.

And definitely check out Harvard Square. Book stores, coffee shops, street musicians, good pubs and restaurants.

I miss Boston. Sniff.

I really appreciate the advice. Like I said, it's going to be my first time in Boston so I want to get things done right. If you see me, I'll be wearing a TkGo shirt (the slogan I'm running under) and a Cubs hat. I know you don't want any fakes in Fenway.

Any other suggestions are more than welcome.