In the Magnificent Mile area, I'm rather fond of Sayat Nova at 157 E Ohio. Good food at very reasonable prices.

My favorite brewpub is Goose Island at 1800 N Clybourn. The beer is phenomenal, and the food is quite good. It's about three long blocks from the North and Clybourn subway stop, but if you have a car I recommend driving, they have free parking.

If you really want to get out of the tourist area, Hopleaf in Andersonville is the best beer bar in town, and they now have quite an interesting menu to go along with the fantastic beer.

I frequent all three establishments and highly recommend each.