Options: usually for components or objects. You have right to choose, so there're some options for you to choose.
Settings: There's a system. It may work as it always do, but it offers some settings for you to adjust its behaviors.
Properties: every object has properties. color, size, and etc. You 'set' settings. and you 'change' object's properties.
Configuration: usually, every system has its configurations, either a default one or a customized one. The system needs a proper configuration in order to run properly. Usually, it has little meaning of user's choice or not. Although you can adjust system's behavior with different configurations.
Preferences: you may prefer a different habit, so here comes the prefer-ences. Every user may have their own habits. Preferences is more like different users sets of prefers. In system level, it may work via different configurations, but on the GUI, we don't say configuration, we say preferences.
In conclusion, for example, in a drawing application, you may say, we change the properties of a circle, a shape. When you start the application, we have three options to choose for how the application would appear after launch. There are some configuration files under the installation folder, some may easy to understand, but some may be very technical, which is not prepared for normal users. Users they just change settings in the menu, to decide how a function works in the application. Settings and Preferences usually don't appear in the same application. Tools that more for efficiency, use Settings more. Applications that more for conveniency, use Preferences would be more friendly for users.
Hope those help.