I make a habit of browsing through any install package and reading the install script before running it. If it looks like any files are at risk of being overwritten, they get backed up. And I create an install log whenever possible.
ImageFX futzes with chooser.gadget and dumps a few things in Libs: as well. Can't remember what else it does. I really wish it would use PROGDIR: instead of SYS: for shared files.