Thanks, Jim! In a somewhat related question, regarding some of what I said above...
"All configuration must be done via a GUI, and must be persistent between runs of the program" seems to indicate that the "configuration" would be perhaps the location of the database (if they selected standalone) or the server and port if they selected "server". I would of thought that you would also store the user preference of "standalone", "server" or "no argument" as well, but it appears you make that choice from the command line, and it's a "done deal" by the time you hit any kind of GUI.
This appears to suggest no storing of "network vs. local" preferences, as these will always be decided from the command line (entering a mode or leaving blank).
For "alone" mode, the only property to store in suncertify.properties would be the location of the local database, I guess. It seems logical that the database shored be stored in the User's working directory, along with their suncertify.properties. However Sun says to provide them with a copy of the original *.db file they sent me. So I am assuming that there will actually be two *.db files, One pristine copy in the location Sun specifies in the hierarchy, and another "working" copy of the *.db, perhaps located in the user's working directory...