Recently there were many cases where Gmail accounts of some people were hacked due to bad passwords or infected viruses on their machines. In that case it is always advisable to keep a backup of all your mails on your computer itself.
Gmail Backup is a software for Windows and Linux that will just ask your Gmail account username and password (safe) and the directory where you want to keep the backup copy of your mails.
You can also specify dates between which you want to have the backup.
For developers -
If you are a geek developer then you can download the python scripts at Google Code and can backup the content the way you want.
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