Top tier in no particular order:
Astral
Great Heights
Holler
Equal Parts
True Anomaly
Local Group
St. Arnold
City Orchard - very good cider
2nd tier:
Brash - I like what they do, but most of their beer are just too...brash
Eureka Heights - A couple of very good beers and usually have a good rotation, but most of their beers aren't for me
8th Wonder - great place to hang out but beers are average
Buffalo Bayou - great place to hang out but beers mostly suck
Urban South
Under The Radar
New Magnolia
Spindletap
WTF are these guys doing? Don't even bother drinking here:
Walking Stick - never had a good beer there
Platypus Brewing - average beer at best
I don't get outside the loop often and haven't visited many of the Greater Houston breweries:
B-52 Brewing - visit if you are ever in the Conroe area. Nice spot and great beer
No Label - not a bad place to visit if you are in the Katy area
Leaving Karbach off the list because they are owned by InBev.