Just write a Python/insert lang here script that will copy your config files to their respective places on all operating systems (eg .vimrc).
For applications, it seems to depend a lot on the OS. Is there a good/easy way to track what apps/package have been installed (for Debian/Ubuntu e.g.)? How could I take replicable snapshots/images of my system (without user data)?
Would something like this even be possible on windows (since it doesn't have a package manager and installs stuff all over the place)?
The next level of hardware independence would be having a system on a USB device to be able to boot into it on different machines (e.g. a light notebook and a gaming desktop) using the same system on both.