My favorites in no particular order:
Two Brothers - This was one of the first craft breweries I got into back in the early 2000's when I started home brewing and I frequented their home brew shop The Brewers Coop. It's been great to see how far they've come since then, I love their beer, food, and any time me and some friends show up at the tap house in Warrenville or the Roundhouse in Aurora, we get great service. Their coffee is pretty tasty too!
3 Floyds - First went there for Dark Lord Day 6 years ago and have been back every year since, and make regular trips out that way for a case or two of something (lately it's been Zombie Dust).
Lunar - Great little place in Villa Park that you'll probably pass by the first time. They do a handful of great beers in small batches, as well as having an enormous selection of other beers on tap and draft. I love the look of their bar and coolers, and I've seen many great local bands play there.
Pipeworks - Haven't had a bad brew from them yet.
Solemn Oath - I'll usually go here Friday afternoons, I work nights so by the time 8AM comes around Friday morning I'm ready for a beer, but they open a few hours later. I loved their Khlorost, coffee infused Wit beer, which sounded like a terrible combination to me at first. I'll usually grab a growler of their Butterfly Flashmob when it's on tap, which is a Belgian style IPA, that's got to be my favorite of theirs.
Goose Island - Not sure what to say about them that hasn't been said already. Except I need more Bourbon County Stout for my cellar!
Revolution - Been a handful of times, and love it. Anti-Hero may be the perfect IPA for me. I'm really happy the Jewel by me in Romeoville now carries some of their beers!
Flossmoor Station - I like the building, and like a lot of these other places the food is good (which is a plus having a girlfriend who doesn't drink), I haven't been in some time, though I've heard the quality of the beer has gone down in recent times. I'll have to go back and find out.
Spiteful - I've only had 2 beers from them, they're pretty new but I've got to love someone that makes a beer called G.F.Y. Stout (which explained on the bottle if you don't know what g.f.y. stands for well then you can g.f.y.)
There are a lot of others that I don't really have a solid opinion on, good but I either haven't been enough, or I haven't had enough of their beer. But I remember not terribly long ago trying to find a new brewery/brew pub in the area was pretty tough, but they seem to be popping up every day now. Need to check out One Trick Pony soon, as well as go back and try Horse Thief Hollow now that they're brewing on premises. Same with Nevin's brewing in Plainfield (from what I hear I shouldn't expect much). I spent about an hour at Haymarket (which is a shame it's less than a mile from my office) and had a few good beers, but would like to go back and try some more. There's so many more, but I feel like I'm just rambling now, so I'll leave it at that.