There are many excellent restaurants in the Boston area, but these are some of my favorites.
Boston
Grillfish - If you want the best fish steak in Boston, this is the place to go. Very fresh fish, grilled to perfection in their open kitchen -- so you can see the tower of flames as they sear your fish on their grill. Prepared with few extra ingredients, the fish and grilling technique speak for themselves. You'll find yourself in a hip, gothic-looking room in the South End, with a huge stone bar sitting along one wall.
Anthony's Pier 4 - Although Anthony's caters to the tourist crowd, and tends to be a bit stodgy, with more traditional New England fare than any other restaurant on this list, I still believe that for seafood there are few better places in Boston. Their service has always been outstanding -- even when 20 of us stumbled in after drinking all day at the Boston Wine Expo. If you are looking for a place to impress your parents, eat lobster and clam chowder, select your wine from an encyclopaedic list, and smoke your cigars in a lounge with red leather couches, you will not be disappointed. They also have a parking lot where you can actually park for free. (Note: the cigar smoking may be out now that Massachusetts has outlawed smoking in all bars and restaurants -- yay!)
Chart House -- In a historic building on the dock with wooden beams and old chandeliers, the Chart House is among my top three seafood picks in Boston. More traditional than Grillfish, but less stodgy than Anthony's, you can eat traditional seafood entrees with a modern twist. Excellent service and atmosphere, a fun place to take a date or a group of friends. I recommend the valet parking.
Terra Mia -- In general, Boston's North End (the Italian section) is highly overrated. Most restaurants cater to tourists, serving vast quantities of very ordinary spaghetti and meatballs and overcharging for the privledge. There are a few gems if you know where to look. (If you don't know where to look, then don't bother eating.) Terra Mia is a very small restaurant with only a handful of tables, but the food is outstanding and modern. You won't find Chicken Parm here, but instead giant open faced ravioli in a delicate lobster sauce. The people at Terra Mia will take care of you in true Italian style.
Brookline
Anna's Tacqueria -- A hole in the wall joint where the employees tend to speak only enough English to tell the difference between a "Super Burrito" and the regular one. Just get the Super Burrito with your choice of filling, rice, beans, and other adornments. For $3.50 you've got yourself a full meal that can't be beat. Unfortunately, Anna's has been "discovered" and now is crammed full of yuppie students who try to order vegetarian entrees. It's much less of a hole in the wall than it used to be, and imitators are appearing. Oh well.
Kokopelli Chili Company (Out of Business) -- Unfortunately, Kokopelli's is no longer in business, it is now an Irish pub. But to honor the memory of my favorite southwest restaurant, I will leave the review. Kokopelli's serves chili of various sorts, in a bowl, over noodles or rice, or wrapped in a tortilla -- along with other delicious southwest entrees. They also have a premium margarita list with about 30 types of tequila, as well as daily frozen margarita choices like prickly pear and mango. The decor is modern and fun, this is a great place to hang out with some friends.
Waltham
Iguana Cantina -- On Moody Street, the Iguana Cantina serves up fairly typical Americanized southwest/Mexican food -- enchiladas, tacos, or fajitas, covered with cheese alongside rice and beans. They also have some original dishes like "Iguana Tail" (really chicken). Some dismiss it for not being authentic enough, but when you are in the mood for some Mexican-style comfort food, this is the place to go. The Iguana Cantina is a very happening place, with a packed bar and a dining room filled with a young crowd. Their frozen "Iguanaritas" and other special margaritas are yummy, and you can get good premium margaritas for a reasonable price. Their other locations have not done well; stick with the original.
Carambola -- By the same owners of The Elephant Walk, which features Cambodian and French cuisine, Carambola has pretty much the same menu minus some of the French options. Their Cambodian cuisine is most similar to Thai, but is definitely a unique taste unto itself. The setting is calm and the food is great. Definitely try the fresh spring rolls if they have them.
Il Capricio -- In a strange location next to a CVS, with a very small sign that's easy to miss, Il Capricio is a high-end Italian restaurant which puts most restaurants in Boston's North End to shame. Impeccable, absolutely professional servers, a full-featured wine list, and very expensive Italian entrees that make you realize all of the Italian cooking you have been working on for years will never hold a candle to the dishes here (at least in my case). Very quiet, romantic atmosphere. That about says it all.
Wellseley
Blue Ginger -- Owner/Chef and Food Network celebrity Ming Tsai describes his restaurant as "East meets West." Very apt, as the food is Asian-inspired yet with modern, New American twists. The signature dish is an Alaskan Butterfish in a miso-soy marinade, and is quite simply the best piece of fish I have ever eaten in my life. You may need to call 3-4 weeks in advance to get a reservation on a weekend: this is definitely a special occasion kind of place. Fairly quiet, but with nice decor and an open kitchen.