Before you decide which option to choose to backup your email, you need to evaluate the importance or operational need for the information. This is a practice called records management.
For more information about records management, please see http://en.wikipedia.org/wiki/Records_management.
For Information about Western University's Records and Archives Policy, please see http://www.uwo.ca/univsec/pdf/policies_procedures/section1/mapp130.pdf
Depending on the percentage of messages which meet your requirement you can consider the various options listed below:
Caution: There are tradeoffs which come with a pop client configuration (e.g. additional time and/or potentially cost to manage the quota associated on the server). Avoid using server side filters on messages which you are looking to create backups of.