Email archiving is hard. I've used all of the solutions above and many more (see below).
In the end, I partially gave up after making several archives and decided to keep a structured master archive on my main work computer (we're talking about 20 GB of email) just to be sure that I have a single copy in a very standard format Apple Mail 4.6 (Snow Leopard edition) with more or less attachments still attached for the last seven years (most Eudora attachments are listed and are findable but are not directly attached to the email). The other advantage of keeping all your mail in Apple Mail is that it's a single archive to search. Surprisingly often I do find that I want to find and review a conversation from 2003 or 2006.
Emailchemy does work although I used Eudora Mailbox Cleaner for my own migration from Eudora (read the notes there and at Tidbits to fully understand just how hard email migration/archiving is). The Weird Kid licenses are so expensive (imagine that if you are using at work, you should be paying about $300 for the privilege, even if you only have a few computers/accounts to migrate).
The simplest solution would be to migrate your Apple Mail account to Thunderbird and the use Thunderbird's built-in archiving tool which does offer unencrypted structured archiving:
Beginning with version 3.x, Thunderbird has built-in support for archiving e-mail. The "archived" messages are moved to a dedicated folder (or hierarchy of folders) within the Thunderbird profile. These are ordinary mail folders (using either mbox or maildir files, depending upon how the account is configured), not compressed files.
Paid alternative options
EagleFiler with its fair $40 license let you do pretty much whatever you like. Great documentation and support available from Michael Tsai is personal and of high quality (I've had good answers myself as well as seeing much public praise for the support). There is an option for storing messages in mbox or eml files:
EagleFiler can also store messages as individual .eml message files, one per message. This is less efficient (for EagleFiler, Spotlight, Time Machine, etc.) but is more flexible because you can drag and drop the messages to different folders to rearrange them. Message files can also be mixed in the same folder with other files of different types, e.g. PDF or Word documents that are related to those messages. You can double-click a message file to open it in Apple Mail.
Mailsteward Pro uses full MySQL (i.e. open source but a bit tricky to install) and costs $100. You can export and merge databases and automate archiving. John Seward's application is pretty geeky. While support is gruff, it is available and personal. As it's MySQL, you'll always be able to get your data out in the format you want.
- MailSteward normal is $50 but uses MySQL Lite so is not suited for large archives.
- Devonthink Professional is $150 and does a good job of providing an archive but foregoes opens source standard mail message or mailbox structure and loses attachments. That said, search is fast, fine grained. Devonthink looks great for a text application. I've owned Devonthink and have the opportunity to use the pro mail import but have chosen not to. With my large archive, I've not been happy with it and have never liked that Devonthink import is truly a one way street.
First I'd try Thunderbird and see if I like its archive format. Then I'd go to EagleFiler. If I was more persnickety and there were still issues bothering me about EagleFiler, I'd then consider full Mailsteward.
I would not fiddle with fragile Apple scripts or
Automator which would need regular renewal and maintenance and are subject to immediate Apple style deprecation.
I'm going to follow my own advice take another go myself with EagleFiler and consider removing any mail older than 5 years from Apple Mail.