A couple come to mind:

The Bluberry Hill Inn - Goshen, VT

A & M Cafe (no website) - Interior, SD (this town has a population of 67) This is a tiny "town" on the borders of the Badlands, but is really well known for the flatbread that's made at the A&M Cafe. It's been featured on The Food Network as the country's best flatbread...been there a number of times myself (family relocated out there a number of years ago), and I can attest it's quite tasty.

Bobcat Bite Cafe - Santa Fe, NM (technically, but it's outside of town in the desert) These guys are known for their hamburger - which is widely considered one of, if not the best in the country. Been highlighted by GQ, New York Times, Gourmet, Travel Channel, Food Network, etc. Make sure to call ahead if you're going, they will sometimes close without much notice...I've stopped by 3x now when they've had "vacations".