I was hoping there was a way to do this. I think this would be really useful, at least for me. I'm still trying to get use to the widescreen and shortness of my macbook screen so I put my dock on the left side to maximize the vertical space (essential when programming).
I think having 2 docks would be great because then I could put one on either side of my screen and do something where all my apps are on the left dock and all my documents are on the right. Also, since my dock is smaller because it's vertical, the icons get really small when I have even a moderate number of apps open. This would greatly solve that problem.