A lot of my favorites have already been mentioned above. I'll re-mention a few here (I'll try to add photos shortly):
FP3 -- this relatively modest project managed to do pretty much everything right. Sets the bar for new developments in existing neighborhoods. Great project...maybe the single best of the lot.
MacAllen Building -- bold, urban, and transformative, it's easily the best contemporary residential building in the city, IMO. And in South Boston of all places. I love this building.
The Brain and Cognitive Science Center (or whatever its called now) and the Stata Center @ MIT-- they are each other's perfect foil. As I've said before, the greatest Boston-area architectural juxtaposition since Trinity Church and the New Hancock.
Zakim Bridge -- Boston's northern gateway, way over-designed and it's a good thing too -- the Big Dig's terranean face does double duty making up for the disastrous Greenway. An instant icon.
Simmons Hall @ MIT -- i know a lot of people dismiss this one as vacuous starchitecture, but I love it. It's the Versailles of college dorms.
Atelier 505 -- I'm no Ron Druker fan, but got to give credit where it's do. He did right with this one. Anchors Tremont St. in the South End quite nicely.
Valentine Houses, Cambridge -- small but notable project by the architects of the Big Dig House, Single Speed Design. I have a soft spot for architects willing to engage and tinker with the local vernacular. These are an admirable attempt at reinterpreting the triple-decker.
Logan Airport's Terminal E -- one of the most spectacular rooms in Boston. See it at dusk, lit in the blue light of the flight monitors.
303 Third, Cambridge -- one small step in the big scheme of things, one giant leap for Kendal Square.
NEU's Building H (is it still called this?) -- NEU's whole West Campus probably belongs here. It provided the university with something it always lacked -- a compelling physical embodiment -- and it transcended its existing campus image that more resembled a military base than a major urban university. Building H provided the added function of, like the New Hancock with Copley Sq., announcing an important place in the skyline, in this case the MFA -- a function it fulfills very elegantly, IMO.
Court House Station -- Silver Line aside, this station with its sweeping concrete forms and stainless steel aesthetic established a new standard for T stations. A raw simple contemporary beauty. A breadth of fresh air in a time when T station modernization means making the place look like a public bathroom.
South Station Headhouses -- Machado and Silvetti's subway portals may be over-designed, but so what. These crystalline hedgehogs recall a time when every subway headhouse was a mini-monument.
The new ICA -- got Boston excited about architecture... and contemporary art. A true Boston architectural watershed.
Also agree with Ron about the Paramount and Opera House. This block hasn't been so beautiful and alive in decades.