After buying and deploying this software at work (around 80 exchange mailboxes, several GB worth of data per month) I discovered there's also a free version for home users.
I've now been using it at home for a couple of months and it is excellent.
You can set it up different ways. Point it to outlook/thunderbird and it will archive everything using that or specify pop/imap settings for each individual mailbox you want to archive.
You can set it to automatically delete emails from the mailbox once it's been archived or leave it as it is. You can also set it to remove only read mail and leave unread mail. It is quite flexible.
You can also setup a scheduled task to automatically archive email at specific times.
MailStore Home® – Free Email Archiving and Email Backup Software for Home Users
For home users, emails are also a valuable source of information. A large amount of data and important files is saved in the form of emails. With MailStore Home you can backup all emails in a central archive, even if they are distributed across different computers, programs or mailboxes. You can do this either on your PC or on a USB drive as a "portable" option.
This way, you will never lose emails again and can search all of your emails extremely fast. You can still reply to or forward archived emails by opening them with a single mouse click in your standard email program.