I only lived in Denver and Boulder, my wife lived in both, plus Ft. Collins. If/when we go back to Colorado, we want to go back to Denver. It's nice for a biggish city (not much crime, pretty clean, lots of stuff to do close to downtown). It's big enough to have almost anything you could want, but small enough the cost-of-living isn't exorbitant.
The light rail in Denver is great. They're working on connecting Boulder via light rail, and a multi-use path too. It was funded by sales tax, and with the economy tanking I'm not sure what happened with that.
The buses aren't bad either. A few bus lines are sketchy (like the 15), but there's another line that runs like three blocks away that "normal" people (not crackheads) use. So there's a bit of learning curve if you want to use public transport. But with 300 days of sunshine a year, a bike or hoofing it is the best way to get around Denver. I lived downtown and worked in Aurora the last time I lived there, and it was faster for me to ride my bike to work than drive. I doubt I put more than a thousand miles on my car in a year, and that was mostly to go skiing or hiking in the mountains.
I truly hate driving, and traffic, and parking, so I'd say live in Denver proper (City and county of) or live in Ft. Collins. If you end up in the 'burbs or Longmont, you'll spend a lot of time in your car, and the traffic in Denver is awful at peak hours.
Fort Collins is a typical college town in most ways, though food and beer are especially good there. If you like living in a city, go to Denver. If you're rather live in a town, Fort Collins is better.
We just spent Thanksgiving up in WI, so I'll put in a plug for Madison. Similar to Fort Collins, but kind of in-between a city and a town. If I had to stay in the Midwest, I'd be fine living in Madison.
PS - Since you'll be drinking a lot at all of the wonderful breweries, being within walking/biking distance, or being able to take public transport is important. I knew a lot of people who've gotten DUIs over the years. CO doesn't mess around with that, unlike MO where I'm pretty sure everyone is drunk all the time. I only know one person who got arrested for biking under the influence, but apparently you don't have to consent to a breathalyzer if you're on your bike, so they got hauled downtown, but then let off the hook.