Trinity Brewpub - This is probably the most well known brewery in town. Lots of good options. House beers are hit or miss and their guest tap list is usually pretty solid. Their food used to be really good however some recent changes have left it a bit lackluster, especially for the price. The patio has a nice view of Pikes Peak. Trinity is the only brewery I have listed that carries other people's beer.
Phantom Canyon - This is an establishment in the heart of downtown. Specializing in English style beer with two beers always on cask. Solid pub fare and good happy hour benefits. Pool, darts etc. on the second floor.
Rocky Mountain Brewery - A bit out of the way in a more industrialized area, this brewery specializes in fruit beers (several world beer cup awards) and strange adjuncts (smore beer...). Their regular lineup is decent, no bottles but they fill growlers of most of their beers. No kitchen but they do have food trucks during high traffic times.
Pikes Peak Brewery - The up and coming brewery in town. Recently expanded their facility to increase capacity and accommodate more barrels. Mostly American style beers, I would say that their regular offerings are the best of the local breweries. Their sampler platter is the best value in town. No kitchen but they have a panini press, pretzels...
Bristol Brewing - Probably the most established brewery in town. Been packaging beer for a long time. Recently moved into a very cool facility that used to be a very large elementary school. For the most part their beer is pretty middle of the road. Good but not great. In the Fall they release Venetucci Pumpkin Beer made with pumpkins from a local farm. It is a local whale and people line up around the block for it. If you get the chance to try it on tap (usually sells out that night) it is a really good beer.
Colorado Mountain Brewery - Pretty generic brewpub, beer is good, food is good, ambience is a bit chain-ish. Overall you will enjoy your time their but you won't actually remember anything special about it.
Nano 108 - Nice selection of rotating taps, 108 per year is their goal (2/week + special releases). I have had a few selections and they seem to run the gamut from really nice to very meh. No total stinkers yet, but definitely not a consistent location yet.
Fieldhouse Brewing - Pretty new, small brewery, south of downtown. I have heard some good things about their special releases but haven't had any yet. Their regular rotation is solid.
Ironbird Brewing - About a block away from Fieldhouse. Pretty good stuff. The session pumpkin beer was really good. They have two taps on cask.
There are several other smaller breweries in town (Great Storm, Redleg, Smiling Toad...) that I haven't been to so if anyone else has something to add, please do so below.
This list is by no means exhaustive nor definitive, please improve it.