You could rather quickly and easily write a shell script to:
- use offlineimap [0] or imapsync [1] to perform a local sync of your mailbox to local mbox files or maildir directories,
- (optionally) use tar or similar to create a single file out of your entire mailbox, and
- use tarsnap [1] to back it up (to AWS) or s3cmd [2] or similar to back it up to wherever you want it.
I used to do exactly that with an additional step to encrypt the tarball (with GPG) before uploading it. It worked out quite well.
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[0]: http://www.offlineimap.org
The majority of serious email get copied (IMAP or for the email server we run, just sftp) to a pair of DVDs on periodic basis as an encrypted filesystem archive. We then stick it in a dvd swapper drive for offline access. The other copy gets put off site.
they have an awesome free trial running right now..