Each time a new version is released, a great amount of time is typically spent scouring the portal.properties file to ensure that new properties that should be set on a system are, indeed, set. Sometimes, these get missed, though. Perhaps it would be a good idea to have the portal-ext.properties generated with commonly customized entries (commented out, of course). I'm thinking some key properties that each customer would want to reconfigure are:
Any .email.from. and .email.address.