Craftsman Table and Tap seems like the best bet in Middleton. I've heard things (good and bad) about The Free House Pub. Steve's on Junction would be the popular choice for bottles, but I've personally never been.
I should add, if you have a car, Madison is RIGHT THERE. Opens up a whole mess of options. Considering they're connected, I wouldn't limit myself to Middleton unless transportation is an issue.
Agreed, the distinction between Madison and Middleton is basically in name alone. If you do go into Madison, definitely check out Riley's downtown for bottles, grab a beer at the Brickhouse next door (they often have Toppling Goliath on tap), check out the Capitol building and take a walk down State St.
Steve's on junction, Steve's on university, Riley's, whole foods for bottles Craftsman has good taps and food Brick house, coopers tavern, brasserie v all have great taps too I was at alchemy yesterday, war mullet and twisted galaxy were exceptional