Whenever I'm visiting Boston there are two and only two food destinations for me, and both are located in beloved Jamaica Plain:
The James's Gate for fish and chips
http://www.jamessgate.com/

and La Pupusa Guanaca (for pupusas, of course)
http://www.yelp.com/biz/la-pupusa-guanaca-jamaica-plain

If I happen to be near downtown on a weekday I'll head over to the North End for calzones and $.75 cups of wine from a bucket at Galleria Umberto
http://www.yelp.com/biz/galleria-umberto-boston

Skip Fanueil Hall - instead, head out of its eastern end, cross over a few streets, hit the North End instead! You'll find incredible shops with Italian goodies for eating out of hand, putting together an easy picnic, or to bring home as souvenirs.

Also recommended: Black Ink/The Museum of Useful Things: not necessarily a kitchen supply store, but you can find really cool pieces there that work as funky kitchen objects.

As for hidden neighborhood gems: at Andrew Sq., on the Southie/Dorchester border, shop (for kielbasa, pierogi, doughnuts) at Baltic Deli & eat at Cafe Polonia or get take out from there and head on over to the beach at Castle Island (finishing that off with an ice cream from Sully's, of course).

For seafood, check out New Deal Fish Market in East Cambridge - great selection, fair prices, excellent service

http://www.yelp.com/biz/new-deal-fish-market-cambridge

I second all the nods at the North End. Lots of great little specialty grocers there and one of the best liquor stores in Boston - lots of hard to find Italian Liquors - V Cirace & Son
http://www.yelp.com/biz/v-cirace-and-son-boston#hrid:R4Mt5AnbsKtCVkmsvvXjfw/src:search/query:liquor%20store%20north%20end

And lastly, a neighborhood gem in Somerville - Daves Fresh Pasta - awesome local pasta store which carries local produce, meats, dairy and great pasta making classes
http://davesfreshpasta.com/

While not strictly a "food shop", Sofra Bakery and Cafe in Cambridge (a more casual off-shoot of renowned restaurant Oleana) offers a variety of Mediterranean-inspired breads and baked goods as well as an assortment of their amazing mezze and other unique items packaged for retail. The jewel-toned carrot jam is a standout.

Another place to stock up on unique food items in Cambridge is Christina's Spice & Specialty Foods, purveyors of all manner of spices, salts, dried chiles, teas, rices, and other ethnic and bulk items. Many of the store's spices are used to create magical flavors like Mexican chocolate at the sister shop next door--Christina's Homemade Ice Cream (a must-stop for any visitor to the 'bridge).

One more hidden treasure, this time in nearby Somerville, is the Dairy Bar at Kickass Cupcakes (which, as the name implies, is a cupcake bakery--and a rather kickass one at that). The Dairy Bar is one of the very few places in the Boston area that sells local, farm-fresh milk (including organic), cream, ice cream, eggs, as well as other specialty items like vinegars, oils, and jams. It's the perfect place to pick up a glass bottle of milk to take home with a dozen of Kickass' signature super chocolate and cinnamon chai pecan sticky cupcakes.

All of this is true.

However, under specialty stores, Russos is glaringly missing. http://russos.com/

My vote would be to not miss the pastry shop Mike's Pastry on Hanover. So awesome and the great boxes with string to go!

Also, best two places I ate were Toro, which was so brilliant. Get the beef tongue. And Sportello, a re-imagining of the lunch counter. Amazing.

Regina Pizza on Thacher St in the North End is the absolute tops!!!

Second to Mike's and Regina's! They are majorly busy on the regular but truly worth the lines. Also Sportello truly does have inspired food. Their bread is served with whipped riccotta, a drizzle of really good olive oil and some golden raisins. I could eat it all night!

Also Santarpios in East Boston for pizza.

Stuff like this excites me! JP Licks or Christina's (in Inman Sq., Cambridge) for the best ice cream.

If you are looking to buy some meats north of Boston, Dom's Sausage Co. in Malden is straight ridiculous.

I have stop now because I could write a five page essay about this.

Blech, I never got Regina's. The thing I missed most about living in Boston is Greek pizza. Some one else mentioned Andrew Sq. There a great greek pizza place there.

I work in the north end, and love polcari's. they have bulk spices, crystallized ginger, dried beans, coffee, loose teas in bulk, and they are so nice.

plus they have 2 varieties of roasted chickpeas which I am now addicted to.

I second dave's pasta, and I heartily endorse russo's-> amazing produce. They told me that they ship to whole foods!

also, for a great lunch, try sultan's kitchen in the financial district. amazing bean salads.

I always found Mike's Pastry too touristy. If you want a really good cannoli, there are much better to be found. Stop by Maria's for a very different experience.

Haven't tried this, but a North End market tour - sounds perfect for food lovers!

And for stocking your kitchen with authentic Italian goods (like 00 flour), track down Salumeria Italiana.

I am surprised no one mentioned Russo's?
A 30-year old, Italian market that has now turned into a super farmer's market with amazing ethnic food (indian and asian peppers and veggies, bresaola and procuitto my italian friends swear by, french cheeses, and all the mushrooms or balsamic vinegars you could find in the old country). They try to only buy veggies from local farmers if possible (making the selection and quality much more extensive in our sadly short warm season) - but the prices are unbelievable. Last summer, I ate heirloom tomatoes almost every night for dinner with fresh mozzarella and sea salt and olive oil (all from Russo's)... and the tomatoes? less than $2 a pound!!

They sell seeds and flowers and plants too, and cut flowers and wreaths, and pots for your container garden. location isn't too great (you need a car) and it is super crowded, but it makes boston worth it. This market alone.

Green Street in Central Sq is a great restaurant. Oleana. Craigie on Main. Ten Tables.

cara_mia got it right with Salumeria Italiana! Also for to-go food, Galleria Umberto on Hanover is a must. If you've eaten pizza in Italy, New York, or even New Haven...please, please, do not bother with the pizza in Boston. It's just not the same, no matter how good the claim may be. Supposedly Neptune Oyster is a great spot where they even teach you how to shuck them. I've seen the market tour wandering around the North End, and it looked pretty good. Also in the summer, SOWA, the South End Open Market is a fantastic spot to wander around and check out handmade goods (and some local foods too!).

http://www.southendopenmarket.com/

Worth mentioning that Boston is an ice cream mecca. I don't know why, but I have never been to a city where ice cream seems to be so important. Toscanini's, Christina's, Herrell's, Rancatore's, Lizzy's, Richardson's, Kimball Farms, I could go on. My personal favorite is Toscanini's (the basil ice cream is amazing, ditto for mint, ditto for molasses cookie) but this is a topic Bostonians will practically fight to the death over.

I also would skip Faneuil Hall. It's a mess of tourists and nothing there is really worth the crowds.

Mike and Patty's on Church Street in the Bay Village is an amaaaaaazing sandwich shop run by a pair of Formaggio Kitchen alums.

Former owners of the Church street spot, Alon and Rachel have opened the Hungry Mother on Cardinal Medeiros Ave. in Kendall Square. If you can get a table, you will be a very happy diner.

There are many many places worth checking out, but these are two of the shining stars in my book.

Emily

Best gut-busting diner breakfast/hangover cure: Eagles Deli in Cleveland Circle. Let's go BC!

Devote a couple hours minimum to explore the North End- Hanover & Salem Streets have shops, restaurants, and cafes that need to be experienced by sight, smell, and taste, but make sure to wander off the main streets as that is where you will find the unexpected gems that make this neighborhood so special. Make a progressive meal part of your adventure- an appetizer here, an entree there, coffee and pastry here, and gelato for walking or cabbing home. Mix in some of the historical sites between food- The Old North Church, Paul Revere's home.

Almost every summer weekend, there's a religious feast/street festival (most are held on Hanover Street but the largest, the Feast of St. Anthony is held on Endicott Street) and add to the North End's character.

North End Favorites:

Bova's Bakery (134 Salem)- I personally think this bakery is better than Mike's or Modern...and it's open 24 hours a day

Polcari's Coffee (105 Salem)- Walking into this store is like walking back in time...amazing coffee and spice selection, entertaining staff

Salumeria Italiana (151 Richmond)- Italian gourmet shop, if you can think of it, they have it

Caffe Paradiso (255 Hanover)- The front of this cafe opens onto the street, perfect place to people watch while enjoying an espresso and tiramisu

Outside of the North End, Tapeo (266 Newbury) has fabulous tapas

Chinatown is great for late night dining and weekend dim sum. Emperor's Garden (690 Washington) China Pearl (9 Tyler Street) have delicious dim sum, a wonderful brunch alternative. Suishaya (2 Tyler) has wonderful sushi at very reasonable prices, they used to have a $25 all you can eat sushi offer, not sure if that's still available as it was a steal.

On Fridays and Saturdays, Haymarket is an outdoor market next to Faneuil Hall (and close to North End) where you can get produce at ridiculously cheap prices. If you're going to be in the area, it's worth checking out.

Oh wow, I think it's time for a trip back to Boston:)

A must for cooks: Dave's Fresh Pasta in Davis Square. They make homemade fresh pastas and sauces which you take home and prepare, they also have an amazing deli (paninis to die for) and have recently expanded to include a wine shop and small specialty grocery with a great selection of cheeses and Italian staples. I also second the recommendation for Russo's market in Watertown.

And should you drive north, Tendercrop Farms in Newburyport is an amazing stop for local, seasonal produce and meat.

as far as specialty food shops go, my all-time favorite is lionettes on tremont st. in the south end. similar to formaggio kitchen, but smaller. he carries only local meats and has an amazing selection.

city feed in jamaica plain is a good place for sandwiches and occasional local produce.

for restaurants - ten tables in jamaica plain and garden at the cellar in cambridge.. they both focus on local, sustainable ingredients and cook up some amazing food.

Boston has a good gluten-free scene going as well!

Elephant Walk in Boston and Cambridge has had a gluten free menu for a long time.

Kickass Cupcakes in Davis Square makes gluten-free cupcakes, and also does frosting shots.

Porter Square has turned into a little gluten-free mecca lately- in addition to Elephant Walk, Stone Hearth Pizza is excellent, as is Zing Pizza and the gluten-free treats available at Zing Cafe/Porter Square Books.

All of the Legal Seafoods restaurants have gluten-free menus, and of course steamed lobster is okay :)

The Boston Globe recommended even more restaurants that I haven't been to: http://www.boston.com/lifestyle/food/articles/2008/04/23/gluten_free_dining_out/

I can't afford the specialtly shops or the real foodie fancy restaurant places but here's my list of favorites that are much more reasonable (i.e. <50 dollars for 2)....

<3 Russo's, but avoid it like the plague unless I'm up really early. After noon the place is packed and the quality of the food isn't as reliable.

<3 Dom's Sausage, my friend's family owns the store. The Patriott tips are effin awesome. I've been trying to get him to steal me the recipe for the marinade, but no dice.

There are a lot of suggestions here for south end and cambridge sommerville so I'll branch out a bit:

NU area:
The Mission on Mission Hill is a fun bar with a tasty menu.

Back Bay:
The Rattlesnake just re-did their menu and is no longer frat boy food. I enjoyed a great grilled watermelon salad there a few weeks ago.

Brookline:
The Publick House is a Belgian style tap house with an amazing beer selection and has great mac and cheese.

Allston/Brighton:
I've heard lots of great things about soul fire.
Also many friends go to hot pot out there.
Also Sunset Grill and Sunset Cantina have awesome cheap eats with great beers and tequilas.

Seaport:
Skip Legal Sea Foods and instead go to the Legal Test Kitchen in the Seaport district (although pricey)

I could go on and on...

For seafood, I'm a huge fan of Mercato del Mare in the North End (http://northendfish.com/). They have a small but well-curated selection of fresh and frozen seafood, prepared dishes and ancillary items, and owners Liz and Keri are just wonderful.

I'll put in another vote for Dave's Fresh Pasta in Somerville. It was on my route home when I lived in the neighborhood, and I still miss it.

In the South End, you can't go wrong with any of Barbara Lynch's places (Plum Produce and Butcher Shop are favorites for provisions), and Lionette's Market (http://www.lionettesmarket.com/) is, for me, worth making a special trip up from RI.

Brix is a favorite for wine and spirits (http://www.brixwineshop.com/)

Favorite cheap eats are Ernesto's in the North End for delicious pizza by the (huge) slice, Boston Kebab House for falafel and Middle Eastern salads, and 163 Vietnamese Sandwiches for banh mi.

Finally, the Boston Public Market is a real gem (http://www.bostonpublicmarket.org/). I love walking there on my lunch break or stopping off on my way to South Station in the evening.

This article and all the great comments reminds me of all the great food sources around here. Did anyone mentioned various local and near-local breweries?

The recommendation about ice cream is so true. I'm happy someone thought to include that. We eat ice cream in winter!

I'm not so sure about the recommendation for local stone fruits--wild blueberries from nearby Maine are certainly a special (and usually expensive) treat. But I grew up in South Carolina so I'm a bit of a snob when it comes to peaches, etc!

Russo's is a fantastic grocery store but a little outside of the city in case no one has mentioned it yet. They have lovely and varied produce, a bakery, cheeses, fresh pasta, sandwiches, etc.

I also really love Dave's Fresh Pasta as some others have mentioned. Their ravioli and homemade sauces are wonderful, and it's always fun to browse their shelves to see what other local goodies they have in stock.

Chestnut Farms does a wonderful meat CSA.

For local breweries and vineyards, not only can you visit Sam Adams, but Harpoon is also right in the city (and they give more generous samples). Wachusett Brewery isn't far outside of the city and has some very good beers. For fruit wines, you can visit Nashoba Vineyard. Coastal Vineyards comes to our farmers market and has some good grape wines too.

Also, I think that Kitchen Arts closed, sadly.

- Salumeria Italiana in the North End
- The Boston Shaker in Porter Square (all kinds of cocktail supplies and a huge variety of bitters)
- Dave's Fresh Pasta in Porter Square
- City Feed in JP for awesome sandwiches and locally made specialty products that can be hard to find elsewhere
- JP Licks (preferably in JP) for great ice cream (try the cucumber) and house roasted coffee beans
- Clear Flour Bread in Brookline (go on a weekend for a big pastry selection that shouldn't be overlooked)
- Harpoon Brewery by the waterfront
- Food trucks at SOWA market
- Grillo's Pickles (I think they have a store front now?)

Definitely avoid anything around Faneuil Hall and beware any chowder that comes in a bread bowl. Stick to cannoli at Mike's (and even then they're not mind-blowing). And our stone fruits are extremely disappointing, (blackberries, too).

Kitchen Arts did close, so sad!

http://cobrandit.com/kitchenarts/

I highly recommend stopping by LA Burdick chocolate shop for some hot (or cold) chocolate and some bars to take home! http://www.confessionsofachocoholic.com/chocolate/my-favorite-chocolate-store-la-burdick

Stay away from the bread bowl and the intensely dull Faneuil Hall!

Brookline is worth a visit for grocery shopping alone (there are some good restaurants there too). Bazaar International Gourmet in Coolidge Corner is seriously awesome - it's a Russian/Eastern European grocery/deli with feta from 7 different countries, more cured meat and smoked fish than I've ever seen anywhere else ever, and a mushroom pate that will change your culinary life.

Also in Coolidge Corner:
Kupel's Bakery, which has the best bagels in town and great rugelach
Mike's Deli for really great pastrami and corned beef
Cafe Fixe has first class espresso (if you can brave the owner, who is the caffeinated version of Seinfeld's Soup Nazi)
Thursday farmer's market, which includes a booth from the Clear Flour Bakery mentioned by the previous poster, and a turkey van with frozen turkey pot pies to die for.

That is a really weirdly photoshopped picture

I second other posting on New Deal Fish in Cambridge- hands down my favorite fish monger. I also agree that Boston is an ice cream mecca. Toscanini's and Rancatore's are my favorite.

If you are in Watertown there are several Armenian specialty markets that are worth trying (Sevan's comes to mind). I also need to give a shout out to Belmont for an excellent beer store in the center (Craft Beer Store) and my favorite donuts: Ohlin's in Cushing Sq. for buttercrunch donuts.

I have lived in Boston for 12 years and I've never had clam chowder in a bread bowl. Is that a thing? I've only had it that way in San Francisco at the Fisherman's Wharf.

Come to Somerville! We have a banging farmers market and tons of people growing/making amazing local food.

Also, the absolute best restaurant and bar in the city are here (in my opinion): Backbar and Journeyman, both in Union Square.

And don't miss Highland Kitchen, it's my favorite, go-to neighborhood spot for a great meal and a delicious cocktail!

I second (third? fourth?) Christina's for both spices and ice cream (ginger molasses is my favorite) and Dave's Fresh Pasta for pasta plus just about everything else. Also, Cardullo's in Harvard Square.

No mention of the Harpoon Brewery down at the waterfront? I love me some Sam Adams and all, but Harpoon definitely needs a mention, too! Their festivals are a BLAST, and they have all sorts of perks for their Friends of Harpoon cardholders.

Two things I miss about working in Boston: Flour and Channel Cafe (fun cafe/gallery combo on Summer St.). YUM.

The Flour Bakery is excellent!

Being English, cannoli isn't a big thing here in the
UK... We walked out to Mikes for cannoli, and a few other delights to merit a box that big... All of it was a disappointment, and we were a bit bemused by the rave reviews for both the bakery, and the cannoli - glad to read that other people find it over rated!

We thought the Gourmet Dumpling House in China town was very good...

Russo's in Watertown, as a few other people have mentioned :) I live in the area so I shop at Russo's frequently. The store is packed on weekends. Forget about going the day or two before Thanksgiving or Christmas - you can barely get into the store, assuming you can find a parking spot, and the check out lines are really long.

Russo's is about a 15 minute walk from the Edward Rd stop on the 70 / 70A bus route if you don't mind the excercise. The 558 express bus runs right past Russo's (with a stop right in front in both directions) but it runs only during the week. There may be a private bus route that will run on Pleasant St from Watertown Sq but it's still all talk at the moment.

Volante Farms in Needham is a good place to buy local fresh produce and specialty items.

Skip Mike's Pastry! It's a tourist trap. A true Italian bakery stuffs the cannoli FRESH. Try Modern Pastry instead as seen on Lidia's Italy on PBS! The cannoli are divine...crispy shell on the outsdie and light lemony ricotta filling on the inside.

Actually, as a correction to FOODEFAFA's post, the Boston Shaker and Dave's Fresh Pasta are not in Porter. There in Davis Square in Somerville. Both are very good recommendations though!

Clear Flour Bread is highly recommended! Best bread around.
Try the Black Sesame Sticks on Saturday/Sunday-- Be sure to get them fresh out of the oven around 11am-Noon! (These are a demi baguette with sesame seeds incorporated into the dough, baked with a sprinkle of oregano, and topped with fresh garlic butter in the final stages of baking)
Also, the rustic olive rolls are to die for. (Not to be confused with the Parisienne/French Olive Rolls) The rustic olive rolls have giant olives in them, as well as a spicy kick.
Their baguettes and ancienne are fantastically good as well.

I lived in the North End for two years and definitely second Ciraces for all of your wine/alcohol needs and Polcari's for coffee, tea, spices, and yummy Italian teats. Though I am happy to have moved back the better coast, those two places alone make me all teary-eyed and nostalgic. Monica's Mercato on near the intersection of Salem and Prince is an awesome (and tiny!) deli. You can get all kinds of meat, cheese, fresh pasta, and Italian snacks. They don't really advertise it, but they'll make you any kind of sandwich you want, too. A sandwich, a mini bottle of wine, and a bag of Italian sweets--a perfect picnic on the nearby Kennedy greenway!

I'm reluctant to say this because I don't want the wait to be any longer than it usually is but the Dumpling House in Chinatown is AMAZING and cheap.

Walking around with a Mike's Pastry box SCREAMS tourist. It is truly not that good. Maria's has the best cannoli.

LA Burdick's is a chain. Head into the South End for the best food. Toro, Coppa, Aquitaine. Incredibly decadent brunch at Mistral (not quite SE, but on the way).

How did this article have no mention of the SOWA Market?

I wouldn't exactly call LA Burdick a "chain." It's a high-end chocolatier that has a few locations, including their New Hampshire base and one retail outlet each in Boston & Cambridge, Massachusetts & also New York City. It's expensive, and a splurge for me, but the chocolates are very good.

I thought the cannolis (filled to order) at Bova Bakery in the North End looked good when I was there yesterday but I bought almond macaroons instead.