We always try to make a stop at The Onion (near the Y, usually, because it's near my cousin's place). Great selection, good pub food, and if you don't want a beer, they have an awesome huckleberry margarita.
The Viking is a great bar atmosphere, but what I have found to consistently produce good food and a great beer selection is Waddell's on the South Hill. Easy to take the wife and kids into, or watch a game with the boys. Honorable mention: the Post Street Ale House downtown has decent beer, both bottled and on tap, and decent food.
The Two -Seven on the South Hill, Brother of the ELK, has great beer selection and good food. Jones Radiator is great and they update their Tap list on Fascebook. They really work hard at getting beers no other place gets. Both on tap and in the bottle. And their PB&J wings ore awesome
The Elk is a landmark and great spot as well, blue spark has great rotating taps, the satalite has great food and a classic (but not so cheap) Dive bar and Iv really wanted to check out Jones Radiator and the Flying Goat, heard great things about both. The bulldog and Jack and Dans are two great GU bars and are about the cheapest spots in town. The guys at the Hop Shop are great as well and I highly recomend checking it out