Boston Restaurant - Coda. Awesome local cuisine and drink/beer list. Very affordable for dining in the Back Bay too.
Outside of Boston - Christopher's in Porter Square Cambridge. Homemade american comfort food at it's best. Lots of rotating beer taps too.
Pizza - Pinnochio's in Harvard Square. The best Sicilian pizza I've ever had.
Greek - The Greek Corner in Arlington. Featured on Diners, Drive Ins, and Dives. Everything is made in house and has outstanding gyros.
Breakfast/Diner - Toss up between Johnny's luncheonette in Newton or the Breakfast Club in Allston. The Breakfast Club is one of my favorites for diners and the food is always consistent with some interesting offerings but Johnny's deviates from your normal breakfast menu and puts a fresh swing on things.
Late Night - Victoria's Diner in Dorchester. Pecan Pie grilled on the flat top is insane and a lot of their stuff is made in house.
Tony and Ann's Pizza - Dracut, I'm a junkie for this stuff, I get extra and bring it back to NYC with me whenever I'm back visiting my family
Kellys Roast Beef - there are a bunch of locations, I always used to hit it up leaving Boston
Gibbit Hill - Groton, someone already mentioned this place, its awesome
Doc Davis Ice Cream - Pepperell, go over the covered bridge on your way there and just enjoy it, home made ice cream at its best, also I used to work there about a decade or so ago
99 in Pittsfield , granted its a mid-top priced chain, its a good price for the food served. The staff morale seems to be good too, havnt seen a waitress with a frown yet, whole family loves the restaurant .
Very good pizza with a nice craft beer selection including organic brews. Upper Crust (Lexington, Waltham, Coolidge) is also awesome--slices and beer, great for lunch. Also like the Mexican style chain restaurants, Margaritas and On the Border--beer and (free) chips for lunch!!!
Rt 128 is getting better all the time for lunch destinations.