Boston has long been known as a great seafood town.   But over the years the cuisine has grown from baked beans and chowder to an eclectic mix of restaurants from upscale to ethnic and everything in between.
 

Seafood

When locals want to dine on seafood they go down to the wharf area. There's a plethora of seafood places there, but you will need to take a cab, as it's not really convenient by T. There's Anthony's Pier 4, No Name, and a whole bunch of others. The North End is another option. The Italian restaurants often have a lot of seafood, and it all comes fresh from the wharf area as well.
 
Turner Fisheries at the Westin Copley Place is an excellent, upscale restaurant.  Jasper White's Summer Shack on Dalton St. next to the Back Bay Hilton has a more casual atmosphere, although it is a bit on the pricey side. The Barking Crab is a casual spot with outdoor picnic-type dining and Union Oyster House near Faneuil Hall is a Boston favorite (not to mention the oldest restaurant in the U.S.). And of course there's the old standby, Legal Seafoods . Though often underrated by locals, the quality of their seafood is unbeatable. Avoid Anthony's Pier 4 , as it seems their heydays have long past them.
 
The Salty Dog in Quincy Market is very good. The fried fisherman's platter is excellent with crispy fresh fish, tender scallops and crispy well-done French fries.
 
Skipjack's is another good one that seems to fly a little under the radar. They have more variety than the typical seafood restaurant and even have sushi.
 

North End

For a romantic and elegant atmosphere, excellent service, and delicious gourmet food, Mamma Maria's on North Square is just the ticket. Sage , on Prince Street is fantastic. It's a tiny place, but it's got that dark, candlelit atmosphere.   Sometimes a bit noisy but it's casual and fun. Reservations are a must, as it's a small place and they fill up fast.

Many say that Pizzeria Regina serves up the best pizza in Boston, and it's hard to disagree. The atmosphere is no-frills, with wooden booths and waitresses that call everyone 'dear.' Their crusts are paper-thin, the sauce homemade, and the toppings range from chi-chi sun-dried tomatoes to good ol' pepperoni.

For the sweet-inclined, the North End offers many possibilities, the most popular of which are Mike's Pastry, Modern Pastry, and Maria's Pastry Shop. While these 3 offer some of the most delicious Italian pastries this side of the Atlantic, the battle of the *best* is still ongoing. (Which means that you really ought to try them all and decide for yourself.)

Upscale

L'Espalier is truly elegant. It says on their website that jacket and ties are most comfortable although not required, but you may as well go all out. This restaurant will be a place that you'll want to dress "up" when you see it and you won't mind one bit, because you'll love this very sophisticated, upscale restaurant as soon as you step inside the door. They've got modern French cuisine and it's out of this world.
 
Aquitaine is another upscale, French bistro, but not too formal. The food is to die for - especially the mussels, pepper steak and chocolate flourless cake (as well as the profiteroles and crème brulee). It's very romantic and cozy and the wait staff is very knowledgeable about the wines.
 
If you want great food and service with upscale atmosphere, try Hamersley's Bistro . The menu changes seasonally, but the roast chicken is always available, for good reason. If there are mushrooms on the menu, you won't want to miss those, either! It's rustic French dining at its best.

Casa Romero is a cozy and romantic restaurant with excellent food and atmosphere. It's not a jacket and tie place but offers upscale Mexican cuisine.

Via Matta offers chef Michael Schlow's (of Radius) interpretration of Italian food and a party-like atmosphere. The pappa al pomodoro (warm tomato soup) is killer, and the 100% Italian wine list is a nice change of pace. For a special occasion, reserve the chefs table: it's right in the kitchen and the staff will feed you all night.