When I commuted exclusively, I always used a backpack. Heavy books, laptops, etc. are just more comfortable, when carrying weight on your hips. On the down side, like all point out, you perspire much more. I have a messenger bag too, but it is more of an everyday bag, as I am not in a position to commute due to the distance and familial obligations everyday. The mess bag works well for most things; however, it is not even remotely comfortable when carrying heavy loads, and doesn't alleviate the 'sweaty back' syndrome. A couple of gallon jugs (growlers, milk, couple of 6 packs whatever) bothers my neck/shoulder after a few miles no matter how I adjust it. A laptop and books doesn't seem comfy either. I have panniers for larger grocery runs and use that as a combo with either a backpack or the mess bag. (No curb hopping here with a grocery load though.)

IMHO the best option is to have a variety of choices and pick the best tools for the job. Over time, the expense of having all is minimal. I tend to shy away from 'single use' gear, so the backpack I use is a general do it all climbing, camping, bikeing, ... The mess bag is my briefcase, lite biking load, everyday bag now, and the panniers are easy to attach and detach so they are mainly for grocery/beer runs or picnic w/ family on the weekends.