It's a matter of installing a 64-bit version of every executable or library on the sysetm, not just the new ones. At that point, an upgrade is the equivalent of a reinstall. In Ubuntu, if you put /home on a separate partition (which you don't reformat during an install), you back up configuration files in /etc, and you save the package list from your 32-bit install, then you should be able to do a full reinstall and have an almost identical 64-bit system to your 32-bit system with only a couple hours' work (not much more time than an upgrade takes to begin with).
Windows, on the other hand, is a bit more complicated because you have to find and install by hand 64-bit versions of all of your 32-bit third-party apps.