I used to like the Marble brewing tap room overlooking the square, but it has moved, but still worth a try.
Il Vicino has good pizza and pretty good beer.
Blue Corn had some good Southwest dishes, but the beer was dissapointing.
2nd Street brewpub was fine.
Beer from Santa Fe brewing is all over, but we have not been to the brewery as it is a little far to get to by foot from where we have stayed.
As far as places to eat, we were disappointed with Cowgirl's BBQ, but they seem to have a good list of beer now. Pasquale's for breakfast or lunch is a must. The Shed has the classic Southwest dishes.
If you can find Le Cumbra beers on tap, have it!
Hope this helps.