really pop3 box? Usually pop3 stores mail on local machine.
on imap system imapsync is really good tool to do this.
maybe there is some tools available: http://www.athensfbc.com/imap_tools/
br,
You are confusing protocol with client....
And yes I'd suggest fetchmail scripted to do this (given it is a one off) so long as the email service your system is going to provide will be storing in whatever the local user storage that fetchmail will be dumping into... or even so long as you can parse the appropriate .mailbox (or whatever) files and import them to your system.
James