Broadway Brewery
Local Brewery, started by some of the same folks from the Root Cellar. Solid selection of house brews, along with a good sampling of non house beers, and a menu showcasing locally grown and raised food stock.
Flat Branch (http://www.flatbranch.com/) is Columbia's original micro-brewery, serving a plethora of house made brews and a few home-made sodas. It offers a wide variety of tasty food items for reasonable prices. Can be crowded.
The Heidelberg a.k.a. the 'Berg, (http://www.theheidelberg.com/) is a bar/hangout close to campus that is enjoyed by many young students. Has a nice outdoor patio on the second floor. Go toward the restroom, and you'll find the stairs going up. Has good happy hour deals e.g., buy one appetizer, get one free. It was burned down in October 2003 (http://atmizzou.missouri....) but has opened again.
Quinton's, Ninth Street. Good happy hour deals with some exceptional sandwiches, and there is never a cover. Best jukebox in the state.