I'm a big fan of Nick's Pub's huge selection, although I guess that might be considered more of a bar than a restaurant.
Best Beer Selection in a Restaurant St. Louis 2012 - Iron Barley
Iron Barley's hearty fare (overloaded "sammiches," schnitzel with spaetzle, oak-roasted pork) cries out for a delicious beer. The south-city institution delivers with a carefully curated selection of craft brews. The boom in local breweries is well represented by draft selections including Urban Chestnut's crowd-pleasing Zwickel lager and 4 Hands' Cast-Iron Oatmeal Blonde Ale. Also on tap are several national craft beers, from universal favorites like New Belgium to those that have arrived in the St. Louis market only over the past couple of years, such as Stone and Green Flash. The list of bottled beers includes intriguing German brews — like the woodsmoke-and-bacon-perfumed Aecht Schlenkerla Smoke Märzen, which is essentially Iron Barley's cuisine distilled into liquid form.