Although I no longer live in Flag these would be my pics:
Brandy's - delicious bakery & coffee, eggs benedict 10 ways, great french toast, superb sandwiches (fresh bread & good meat) with nice sides. They were on DDD and I guess they serve bistro type dinners now also. They were on Cedar in the Safeway center.
Beaver Street Brewery - We usually just went for the beer sampler and the delicious fondue or other apps. The dinners are a bit spendy for what you get, but still better than a chain. My MIL is a supper fan of their bread pudding, I think its a little dry.
Kachina or La Fonda - Authentic AZMex food. No it is not authentic Mexican its a mix of MexAmerican and Native American. The Green Chile is uniquely delicious, scratch made and not too spicy its a bastardization I still crave, on a cheese crisp (an open faced crispy quesadilla) or enchiladas is my fave.
Mormon Lake Steakhouse - Aged beef, scratch made sides, operated by locals, delish.
Mike and Rhonda's - Breakfast only, huge portions, fluffy biscuits, creamy sausage gravy, real ham steak and red eye gravy. Always packed. The East side location is best.
Ms Zips - A delicious greasy spoon. Their specials are always homey and good.
Bun Huggers - Charbroiled while you watch burgers on fresh buns with fried sides and build your own burger bar. My DH still craves this place, its a Northern Arizona institution. East side location is best. West side is for college kids and tourists.
The Hideaway - For the true bar crawl/collegy experience with good thin crust pizza and wings to order. Yes I do remember when the wings were 10 cents each, they're still good.
While we did try several finer dinning and ethnic restaurants we never went to any twice accept for the Szechuan Buffet for our 1950's Chinesey fix, but there are bound to be more options now. Oh and if you've never had Indian Fry Bread you can't get much more local than that.
There is no Eastside Bunhuggers only the one on Milton. If you are looking for a "snackbar" type burger then this is your place. Think summercamp, poolside, greasy, soggy fries, you get the point.
For burgers, Diablo although new is fantastic utilizing all local ingredients including the beef. It's a great addition to the Flag dining scene.
Cuvee 928 is a wine bar with good appetizer and sandwich selections. If you are into wine then this is a good choice.
There are a few "fine dining" choices. Don't come to Flag with "big city" standards though. You'll be disappointed. Cottage Place is probably is the best for food and service, but many accuse it of being "old school". Well it is, but it's quite consistently good which I can't say about other fine dining venues such as Tinderbox, Brix and Josephines.
Pasto is a worthy Italian venue with some local twists. It's right downtown in the square. I've had some good and always interesting meals there. Great Italian wines too.
That's good for now. If you have specific interests let me know.
I'll add one high-brow place to the list (though that seems idiocyncratic for a laid back town like Flagstaff. Cottage Place could easily compete with any of the small, chef owned restaurants in the valley. and the wine list is wonderful, and not as inflated in price as we get down here. Recommend it for a lovely, albeit expensive, dinner out. Great service.
126 W Cottage Ave, Flagstaff, AZ 86001