Mac: Backup Mail.app

Copy the ~/Library/Mail folder If you are using a POP account, the simplest method of backing up your Mail.app data is to simply copy the ~/Library/Mail folder (the tilde [~] represents your home user directory) to a separate backup location -- your .Mac iDisk, a CD-R(W), DVD-R(W), an external hard drive, etc.
Your best bet is to perform this process manually by dragging the folder to its new location, as many back tools have been shown to improperly copy Mail.app's data files and folder structure.
If you ever want to restore mail backed up via this method, simply replace the ~/Library/Mail folder on your new Mac OS X installation with the "Mail" folder you've backed up to a separate volume.