And what client protocol have you been using on this Lunix box then?

There are several way to do it.

1.  First question: where does the mail exist?
2.  Second question:  do you have an LDAP server on your eunuchs box?

If the mail exists only on the server (I'm guessing this is a possiblility
due to the webmail), then the problem has two parts;

   1.  How to move the mail accounts.
   2.  How to move the mail.

If you have an LDAP server on you current email server, then I'd recommend
the Transporter suite.  This is very similar to using mailmig in Exchange
2003 to do an IMAP migration.

If you are manually migrating or creating the mail accounts, then you could
also consider scripting on the Linix side.  It's fairly trivial to parse
var/mail/user, read the headers, and forward mail unread mail, or all the
mail for that matter.

If mail has been pulled off the server and exists on the client, then you'll
need to forward mail from each client to the new mail account.