Let's see- I'm a fan of Town Hall. Great beer, pretty good food. The Happy Gnome isn't a brewpub, but it's got a phenomenol beer selection. The food there is good. SeeBee John took Bob and me there for dinner a couple of weeks ago, and we were very pleased with the food as well as the great tap beer.
Barley John's is ok. My favorite "find" in Minneapolis was Surly Brewing. I loved all of their beers, which are available in 16 ounce cans or on tap in many places. If you can get to their tap room, they had a ton of stuff available that I don't usually see- a great mild, for one.
One other beer we find in a package store was by Lift Bridge Brewing. It's in the Minneapolis area, and I've never found it available any place else. Their pale ale was called Crosscut Pale Ale. Bob really enjoyed it. It's a very grapefruity citrusy pale ale, with grapefruit peel in it.
Flat Earth is another great microbrewery. If you find one of theirs on tap (they don't bottle), or can get to their brewery for a growler fill, it's worth a try! I liked their Belgian pale ale and various other beers that I can't remember now (it was the last stop on a 4 brewery tour!).
Stubbs & Herbs, near the University of Minnesota, has a pretty good tap selection and a LONG happy hour. I think the pints were like $2.50 or something. Food was good- sandwiches. Next to Stubbs & Herbs is a good Vietnamese restaurant.