Tricky, this, as there's no one single consistent style followed by all applications. As you say they are (broadly) synonyms.
In truth it doesn't really matter so long as your expected audience understands what you mean.
The biggest difference is between Properties, which usually affect a component or object, and the others, which affect the whole application.
Following an approximate lead from Visual Studio and other Microsoft products:
But there's no single rule.
I'd suggest you use Properties for object characteristics and Settings for everything else that's application-wide.
These aren't set anywhere, but I figured I might as well chip in my 2¢ on the topic. When I see these in an application, this is what they imply to me:
I think that one point of view is missing here namely the relation between configuration/settings/options/preferences.
To me a configuration or preferences contain many settings or options so there can be one setting or one option.
You usually say "Change this option/setting" and not "Change this preference/configuration", don't you?
When someone says preferences or configuration I understand it as a set of settings or options.
One thing that I don't see in the answers here (although bobince alludes to it) is that you should consider what is typical for your environment/operating system. For instance on windows I think "Options" is the most common choice even though many programs use different words. Likewise "Preferences" for mac os. Android OS uses "Settings"
So bottom line, use what is most common for your environment.
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