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Save command saves the layout of the current thinkparts query view dialog as defined through the View Properties into a file named after the currently selected catalog. The location of the file is indicated in a confirmation dialog that informs you of the action being correctly performed.
You can find this command a a button in the thinkparts query view dialog that opens when you run the Open command on a catalog of parts.
Whenever a query view is started on a catalog, thinkparts searches for a file named after the selected catalog, and, if present, uses it to display the query view results. The layout of the query view can be customized with the View Properties command.