Would it be a big deal to call user-defined scripts during startup and closing portableapps.com?
I'm thinking about looking if a specified batch file (for example startup.bat or shutdown.bat) exists in the Data folder.
If it doesn't exist, skip this point.
If it exists, execute the batch file before going on as usual.
Thils will give the user a possibility to define whatever he wants to do during startup or shutdown of portableapps.com without bothering you with "i need this new feature!!".
I think batch will be the best solution because every windows can handle them without requirements. And if the user wishes to use another scriptlanguage (like python or even java) he will be able to write a call of his programm with the corect parameters (like the path to a portable python interpreter) into a batchfile.
This would also cover the request Global Environment Variable Possible? in this forum because Enviroment Variables could be set and unset with batch scripts, too.