Seaport,
It will probably depend on which PLC you are using. Some PLC software allows you to add a 'version' number. You could then keep a file somewhere with a list of version numbers and what changes they brought. You can sometimes add 'comments' to the program, normally by going into the properties of it.
You could always just write a Notepad file and store it in the same folder as the software...
Apart from that mate, I'm not sure...