The location of your wife's job will be the key here. For example, you do not want to be living in Boulder if she has to commute to the Tech Center, Aurora, etc. (or conversely, living in Denver with a commute to Boulder could be even worse). I think you need to figure out where she's working before you can hone in on the best location to live.
If she has a job northwest of Denver or on the US36 corridor, the obvious choices based on your criteria are Boulder, Louisville, Lafayette, and Longmont. Renting in Boulder is actually not that expensive relative to those other towns, and for a couple in their 20s with no kids might be worth the slight premium. (Buying a place in Boulder, however, is a different story.) Although depending where you are coming from, you may not find any of these communities "affordable."
Edit to add that as a runner, I would choose Boulder or Louisville over any of the other places mentioned. Better trail access and variety, as well as a bigger running scene (races, clubs, etc.) if that's important to your wife.