Square One Brewery and Distillery gets my vote. Of course they are located 2 blocks from home so I often walk there and stumble home. They have a decent menu and you can't beat $2 Burger night on Tuesdays.
I like the Schlafly Tap Room better than the Bottleworks if just for the atmosphere. Plus they also put some of the crazier stuff on tap there.
Schafly, O'Fallon, and Square One are all really good! The Hill Brewery in Ferguson makes some good stuff, and they aren't scared to try different things, and be a little more extreme. The brewer from Trailhead is the head brewer(from my understanding), and he has a lot more flexibility here. One interesting brew that I've never had elsewhere is a Pecan Brown Ale, that they make at Hill Brewery. Good stuff! Trailhead makes some decent beer too, just nothing hoppy...I am still in amazement that they don't even have a pale ale! They have a great brown though!