I even go to such lengths as install a program, then copy it over to another folder and uninstall it, and then use it from that custom folder thereafter. This way, I don't even have to reinstall anything if I should happen to set up a new version of Windows. Nifty.

I wonder if it would be feasible to detect software deployed not as a standard installation, but rather as files placed on disk.
I tend to use this kind of installation if only it is provided by software authors (fe. Ant Movie Catalog or VLC Media Player) to keep system cleaner.

This feature would require of course pointing SI to a path where software is located.