The simple process is: create a smart mailbox, archive that smart mailbox's content and then delete all the mail in that smart mailbox. In greater detail:
Smart Mailbox
Mail has an interesting facility called "smart mailboxes." This is a virtual collection of mail, derived by following various rules. Create a smart mailbox by clicking the?[ + ] icon in the bottom left of the Mail interface. Choose "New Smart Mailbox..."
Using dates to identify old mail is a good idea. Name the mailbox appropriately, and then add filter rules to populate the mailbox. For example, to collate all email received before the end of 2008, add:
Archive
Right click and choose "Archive Mailbox" to generate an mbox format mail archive. You will be prompted for a location to save the file to. Make sure that the file is being backed up by Time Machine, if you're using the OS X feature.
Delete Smart Mailbox Content
Select an email from the Smart Mailbox. Press Command-A to select all the email in this mailbox, and press the delete key to remove it. Right click on your trash mailbox and choose "Erase Deleted Items" to finish the deletion process.
Note that simply deleting the Smart Mailbox folder will not delete the email too, you must follow the above process, selecting the mail content manually and deleting it.
Restoring an Archive
Within Mail.app, choose?File > Import Mailbox > Files in mbox format and select the mail archive. This will restore the email into Mail, allowing you to view it again.
