There's lots of stuff above I'd second as well, especially Ron's nominations of Charles River Park/the West End and City Hall, plus Tremont on the Common, the Midtown Hotel, and the Darth Vader Building.
I'd also add the areas of Boston that are unlivable/unused because of transport infrastructure: the SE Expressway ramps near Chinatown/S Station, the similar ramps near the garden, the Pike, and the Central Artery/Greenway. Basically all the handiwork of the BRA (why does this organization still exist? it's like having Robert Moses continue as head of NYC's DOT) over the years...