A few personal favorites (I’ll try to keep the list updated).
Island Creek Oyster Bar - Crowded, shi-shi, expensive, loud? Sure! But also the most consistently amazing oysters, raw bar and food. This is where I go when I want a great meal. Never disappoints. Getting a table can be a bit tricky (unless you are a regular). They take reservations but typically only for the early or late slots. Around 9:30 you can usually grab a seat at the bar. (Kenmore/Fenway)
Alive and Kicking - Lobster shack. No frills. Outdoor seating. Great lobster sandwiches or steamed lobster. (Cambridgeport)
Flour - Bakery with great lunch options. Cinnamon rolls are amazing. (Multiple locations, South End, Cambridge …)
Render - Really good coffee, minus the attitude you encounter in (almost) every other good coffee shop in Boston. (South End)
Row 34 - Run by the same people as Island Creek Oyster Bar (see above). More industrial with slightly different menu in hip neighborhood. The food is just as awesome! (Fort Point Channel)
Sportello - Have only been once, but loved the decor and food. Simple Italian dishes with an effortlessly cool vibe. (Fort Point Channel)
Giulia - Amazing Italian in the Harvard area. Need to book (or come late and get an uncomfortable Bar seat, like me). (Harvard Sq)
Toscanini - Late night ice cream spot. Good typography. The NYT’s quote in the window is BS. (Central Sq)
Red Sox - Do it! Eat a hot dog. Get a ridiculously overprized can of beer. Suffer in the tiny seats. It’s awesome.
ICA - It’s not the MOMA NY, but great views into the harbor and some good art.
MIT campus - Great buildings across the MIT campus. And what’s even better is that MIT has an open door policy. Almost all of the buildings are open during working hours (and many 24/7). Highlights include the old and new MIT Media Lab buildings, Frank Gehry’s STATA center, and the new student dorm in West Campus.
Harvard Bridge/ Charles River - Slightly misleading name, this is actually the bridge that takes you to the MIT campus (first). On a nice day, walking around Charles river and crossing the bridge are two of my favorite things.