Surly, Summit, and Flat Earth come to mind for tours and great beer.
The stores like Blue Max have a GREAT selection of beers and make sure you stock up!
Surly comes in 16 ounce cans, and is probably my favorite brewery in the US. Every one of their beers is awesome, and the tap room is wonderful as well.
If you get the chance, the Rock Bottom downtown is really better than the average Rock Bottom. Town Hall is a wonderful brewpub and the food is good as well. I love Happy Gnome and Muddy Pig for bars with excellent selections. Near the college is Stubbs and Herbs, and they have great sandwiches and good beer on tap (not a brewpub).