I'd like to archive most of the past 15 years worth of business related email messages. Over the years I have migrated them between various programs, and each time was tricky due to different file formats that these programs used.
I'm currently using The Bat!, and it gives me the following Save or Export options:
If I had to pick, I'd pick mbox, mostly because I have lots of existing scripting available that can work with that format and convert to/from maildir format as needed from a server perspective. It's a common mail format that most desktop mail programs should be able to handle too. Worst case, if you ever needed mbox converted for a specific mail program, that should be easy to get done.