I no longer have a need to upload email to Gmail. But, I'm posting this as an idea for others to consider.
CloudPull is a Macintosh application that will backup and restore Gmail.
I'm thinking that if you want to move your mail from a regular Gmail account to a Google Apps account then perhaps you could do this by backing up the the Gmail account using CloudPull and then "restore" the backup to the Google Apps mail account via an IMAP client.
Just a crazy idea that came to me.
I have NOT tried it. I don't know what it would take to make it work.