Rahul Mahajan has written a great document to demonstrate where does the tcode lists in your SAP GUI get stored. You may wonder how does he found that place.
I will show you a generic way on how to find the place in the OS registry where stores all the settings related to SAP GUI.
The basic idea is to export the registry as a snapshot before SAP GUI setting is changed, let’s say before change snapshot. And change some settings or do something via SAP GUI, and export the registry again let’s say as a after change snapshot. Compare the two, the difference what you are looking for.
You can use File->Export to export the node HKEY_USER and its children: