I grew up in Iowa City, went to college in Decorah, lived in Madison for six years and now live somewhere in between.
A few things to consider between IC and Madison, based on my experience...
Do you like water and lakes? Choose Madison.
Do you like a holier-than-thou liberal attitude? Choose Madison. (I'm pretty liberal, but I couldn't stand the attitude there sometimes. IC is just a typically liberal college town.)
Madison has the advantage of being closer to great outdoor recreation than Iowa City.
Madison has the advantage of not feeling quite as shut down in the summer as IC does once the students leave.
Madison feels like a much bigger city than Iowa City so probably offers more opportunities for cultural "stuff."
Running is pretty good in both Madison and IC.
I absolutely love Decorah as it's a great mix of small town and college town feel, with an equal mix of hippies and rednecks, some great breweries and restaurants (especially given its size) and the trail running is spectacular. Plus, it's beautiful. I'd move back there in a second.
Champaign? Meh. Bloomington? That's in Indiana and, well, my friends in Indiana are all looking to escape the state. Don't know much about Ann Arbor. LaCrosse was mentioned and that's worth looking at.