Revolution Brewing - solid brewery, their Porter is definitely worth a look-see-taste; I believe their pub serves food but I've never actually made it there. Near the northern (i.e., toward O'Hare) California stop on the Blue line. Don't ask me why one line has two stops called California.
Half Acre - a young 'un; they only opened up about 3 years ago. Used to be my neighborhood brewery so I may be partial, but I think they do really good things there. They opened a fairly bare-bones taproom this spring, and I had a gas of a time when I did their brewery tour a couple summers back. Closest train stop is Montrose on the Brown line.
Goose Island's brewpub goes without saying. I've never been to their Wrigleyville location, but their (slightly north of) Goose Island location used to be a favorite stopping point on the way home from work. On beer terms, though, if you have to pick one to miss this is probably it. They do have one or two local-only brews, but thanks to the influence of a certain large brewing conglomerate who shall remain unnamed, most of what you'll see here is probably even available at McMurdo Station by now. Short hop from downtown via public transit, though - take the Red line to North/Clybourn.