Ale Asylum and Karben 4 are good brewery stops (they're also about the only ones - Madison has less breweries than you'd assume). I used to be down on Ale, but the wife and I were in town about a month ago and they had a really great IPA line up.
The Old Fashioned is one of my favorite places on the planet. They have excellent Bloody Marys, a full line up of Wisconsin beers, and the food rocks. Amazing cheese curds, and you can get a braunschweiger and onion sandwich with Muenster cheese, grilled summer sausage, and sauerkraut.
Tipsy Cow, Hop Cat (their El Bait Shop), and Paradise Lounge are all fun bars. Paradise is a dive with cheap beer and a loud juke box. It's pretty much perfect.