Mail Steward
With over 30,000 emails in my Macintosh Mail application, searching had slowed to a crawl. My Mail.app seemed to be slower and buggier lately as well. Guessing that I had too many email messages in the database, I tried a highly-recommended email archiving program called MailSteward.
It's easy to use. Just click the "Setup" button and then click on a few checkboxes, then click "Store email in database." It took all night for it to index my files, but once it finished, I was able to clean out my email app and start from scratch. Now, at the end of each day, I click "Store email in database," button and MailSteward sucks all the new mail from that day into its database. $29.95
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A cheaper alternative: make a new mailbox, drag a bunch of mail into it. Quit the app, find the mailbox in /YourUserAcct/Library/Mail/Mailboxes. Burn it to a disk or whatever and delete the original. Now, if you need something, you can pop the disk in open the mailbox from Mail.
By the way, you can't have "too many email messages in the database", because mail is stored in flat files, not a database. Mail Steward *creates* a database, then imports mail into it.
And like CrackWilding said, you can just drag your mail elsewhere, or copy it from /Users/yourusername/Library/Mail/pathtowhatevermailbox/ to some other directory, which, unlike Mail Steward, is free.
I haven't had any issues on my box…I have over 350,000 e-mails in my copy of Mail.