I encountered the need and implemented solutions to save user configuration data several times over in the past.

Today, prompted by a recent query, I'll point out two of them, and some other exciting and interesting stuff as well:

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Listen to the half-hour BIMThoughts interview with Anthony Hauck, Director of Product Strategy at Autodesk, talking about what may or may not be coming in Revit’s future:

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Question: I used the .NET settings file, e.g., xxx.dll.config, to store user and application data.

Unfortunately, it does not work; manual modifications are ignored.

Apparently, it is only active at the application (.exe) level.

The project simply retains the default values for all class library projects.

I still can’t find a workaround up to this moment.

Do you have any suggestions how a Revit add-in can store external configuration data that can be modified by a user?

Answer: Yes, definitely. Thank you for bringing this up.

There are a number of ways to address this, for two of which I can present ready-made implementations on GitHub:

First, to be clear, let's rule out the usage of the top-level application configuration file revit.exe.config. That would be a very bad idea, for a large number of reasons.
Implement your own text format configuration file storage and parsing.
Make use of the .NET XML configuration file storage and parsing functionality.

Storing user settings in a config file via the .NET ConfigurationManager and OpenMappedExeConfiguration methods:

Search the two blog post discussions listed above for the word 'config', and look at the Config.cs configuration file implementation and usage in the DirectObjLoader GitHub repository.