As for best combination of food and beer...
Obvious choice is Row 34. Seafood and killer taplist with a lean towards sour offerings.
Love the elevated pizza and beer combo at Brewer's Fork or Picco.
The main "gastropubs" in the city, Lord Hobo, Deep Ellum, and Publick House all have awesome beer and fairly good food. As for actual brewpubs, Cambridge Brewing Company is always worth a stop. Their food isn't quite foodie level, but it's fine. You can also bring take-out food to some of the breweries like Night Shift. I've picked up Rincon Mexican a few times on the way there.
I love the burger at jm Curley and they've got an okay (but smaller) beer selection. Right across the street is Stoddard's with a better selection and down the road is Tip Tap Room with some exotic meats and good beer. Both the last two I feel try hard but don't quite get there with the food.
North End has a bunch of great italian restaurants but pretty devoid of beer. For food, standouts to me are Panza, Taranta, and Neptune is pretty good (but I'd rather go to Row 34 than Neptune if beer is a consideration).
No beer (I don't think), but an under the radar spot that my girlfriend and I love is Orinoco in South End. Love me some Venezuelan.
For more foodie places, the Boston Globe's "Munch Madness" at least lists most of them (
http://www.bostonglobe.com/brackets/munchmadness2015). Craigie on Main, Alden & Harlow are some favorites from here. Both great food and better than average beer selections.