You didn't say what mail app you're using and which OS X version, but lets assume it is Mail and Mavericks ...
I regularly backup /Users/myname/Library/Mail/Vx/Mailboxes to a dedicated 64GB flash drive; you might also want to backup your attachments - /Users/myname/Library/Containers/com.apple.mail/Data/Library/Mail Downloads/
If I need to access a particular email, I either search for keywords/dates, or if I know which folder/subfolder it should be in, just secondary click on it and open "Show Contents" in a new tab (depending on some settings in Mavericks, double-clicking might not work for some system folders, hence 'open in a new tab').
Any message from such a backup can be merged, moved or copied into an active Mail folder structure on another system, which is very convenient, just double-click on email file and select desired action from the top menu.