Ale Asylum for brewpub - thank me later and don't go there for the food. Old Fashioned has a great draft lineup. Great Dane is a must, but the last time there no stand outs. Tyranena blew my socks off at one time, on our last visit it barely moved a lace. Be sure to go to Come Back In.
As was mentioned, Doty's is good for burgers, New Glarus if you are into the self guided tour kinda thing, if you head there you might as well swing through Mt. Horeb and go to Grumpy Troll. Capital has a great beer garden, but there beers all pretty much taste the same except for a select few (sorry, they do).