It all depends on when you're going. Making definitive plans for Boston is very weather dependent. For the record, the weather's supposed to be absolutely miserable for the next week, but it's looking to be gorgeous next weekend.
It also depends on what you're into. Boston is a rather diverse place and there's tons of things to do. Looking through your post history, it seems that you dig photography. Would that be accurate?
If so, that's going to be a great advantage for you. There are so many disgustingly good photo ops in this city. My best recommendation on that end? When you get into town, take the red line on the subway to Kendall Square (This is just outside the city proper and into Cambridge). From there, walk towards the river (Just ask someone when you get off) and walk across the bridge (Longfellow Bridge). There are a ton of gorgeous views on both sides (Though you can't cross from one to the other from on the bridge, since the train goes over it). The one caveat here is that this is time dependent. If you're going very soon, you won't be able to do this properly. You'll get good views of the Eastern side of the city, but the bridge is undergoing heavy maintenance right now and one side of the bridge is closed to pedestrians.
Once you cross the bridge, you're in Boston. From there, you've got two potential quality routes. You can either keep going straight and you'll pass through Government Center after a fashion, which is good for cityscapes and the like, or you can follow along the river across the Esplanade which has great riverviews and more trees and parks. I'd recommend the former, as it gives more variety.
If you follow along Cambridge Street (Going straight), you'll come across Boston Commons after about fifteen to twenty minutes. From there, I'd recommend cutting across the park. If you cut straight through, you'll get great park shots and you'll be able to see the swan boats and the Public Gardens and it will lead you to the already recommended Newbury Street. The shops are all well and good, but Newbury Street is gorgeous to look at. It's got a good earthy vibe to it and there's some beautiful looking churches. If you follow Newbury Street to the end and take a left, that'll lead you over near Berklee. If you take a left just before there, it'll lead you towards the Prudential Center and Copley Square, both great areas for pictures. You can also ride the elevators to the top of the Prudential Center for some great shots (Though you have to pay for the top floor's access, just below that is fine too). Prudential and Copley Plaza have some great shopping too. If you follow that road straight down, you're going to run parallel to Newbury and come back to the Commons, which you can take a left just shy of to get to the aforementioned Esplanade.
This route will give you a pretty all encompassing walk of the city's best landmarks, though there's other areas worth exploring. Two stops north of the Kendall stop is Harvard Square. Just behind Government Center is Fanuel Hall and just past that is the harbor and the Aquarium. Past Newbury Street is Fenway Park which, baseball fan or not, is a great sight.
Considering the ugly rain today, I don't plan on going out for lunch, so I'll see if I can mark a couple things on a google map in MS Paint for you on my lunch hour.
There's many other things to do, great music, great food, etc. Maybe give some details and I can provide some better advice. Just popping in and saying "I'm going here, what should I do" is entirely too subjective to give any decent advice for.
Edit: Also, are you planning on staying in the city itself, or one of the suburbs? Some places are easier to access from others and that can have a big effect.
The aforementioned Aquarium is great, but also, there's the Museum of Science, which is a blast.
