When the Enterprise Geodatabase used to be three tier, with the ArcSDE running, you had the option of shutting it down and restarting. This had the added bonus of stuff used to get cleaned up in the restart. For example, Log File tables that may have been created under a session, but not dropped when a connection terminated abnormally. The same goes for when KEYSET tables are created, or when stay connections may have been around.
With the two tier connect - the database is not restarted, and thus these items have a habit of accumulating, and needing to be cleaned up manually. It would be good to have some sort of Restart or Clean up script, that did the same thing the old restart used to do.
In a similar fashion, if you have been using and Enterprise Geodatabase (say Oracle) for a number of years, there can be a problem where feature classes may have been created in third party apps, or created in say Oracle Spatial and registered with the Geodatabase, but subsequently removed, but leaves entries in the Geodatabase tables.
It would be good to have a Clean geoprocessing tool that reports on the integrity of Geodatabase entries and can clean this up (sort of like a Windows Registry clean).