You can go through Roxbury during the day, its just a little rough on the eyes. There's an excellent Scottish restaurant (The Hayne) over by Jackson Square.
Further down the Orange Line is Forest Hills, which is where the Arboretum is, a very nice outdoor tree museum.
The Oyster House in Downtown is good, but its very crowded, so is the Green Dragon usually. Another place would be Jacob Wirth on Washington Street over by the Boylston Stop. (Its german food).
Coolidge Corner on the green Line has, Lemongrass (Thai), pubs, and a nice little cinema. There's a weird toy shop over there that I managed to find some rather old board games, like the copy of Diplomacy with pewter pieces. Brookline Booksmith is an interesting indie book store with a slight Jewish bent.
I should warn you, Chinatown will disappoint you, but it still has some Chinese restaurants left.
There's a path along the Charles river which is also a nice walk, as is the holocaust memorial trail (though solemn).
Boston Public Library is free to go in, and beyond books they have a few displays up and a rather nice fountain with benches.
Quincy is fine too.... during the day, but there's fuck if anything to do there besides Wollaston beach.
If you go to the MFA, their best and most unique stuff IMHO is the Asian specifically the Japanese exhibit, which includes a Buddhist Temple. They also have some interesting Sargent pieces, particularly one which they also placed the vases from the painting next to it.
But get a map and prioritize, if you have allergies the museum may trigger them. I'd avoid the modern art section.
Another commuter rail trip would be Plymouth. You don't want to drive anywhere near it and the cape in the summer.
A third is Concord, MA... reachable via North Station. The cemetery has Emerson's grave... boulder, as well as the more normal graves of Henry David Thoreau and Louissa May Alcott. The town center has some interesting restaurants. There's also a sort of trail that leads to a rather interesting reservation behind Concord, a swamp and lake area with a decent amount of Herons nesting there.
A bit of a hike, but you can take a bus to Watertown Square which has an Armenian Library Museum of America, and Wild Willies (very good burgers and homemade root beer).
Speaking of gay, I believe they have a ferry from Boston to Provincetown, its a gay/transgender sort of hangout.
Hope that helps.
Edit: Almost forgot - Rhode Island does have some points of interest, if you're a lovecraft fan the guy is buried in Swan Point which is sort of reachable from the Providence Train Station (though a bit of a walk)
