It's fairly easy to figure out which files in
~/Library/Preferences are used by Apple applications and which app.
All the Apple ones start
com.apple and then almost all continue with the name of the application or part of the system that they are a preference for - some examples
With the less "specific" ones once you know more about how the back end of the System and Finder hang together you start to realise what they are, for example
com.apple.LaunchServices.plist is the one that defines your personal URL and file type handlers as that is done by LaunchServices.
Mac sysadmins tend to slowly get a list of the more important ones as we use them to push preferences out to our managed Macs. If all else fails I use InstallEase, the free utility from Absolute, to snapshot a Mac then change a preference and do another snapshot to see what changed.