I configured my Google Apps e-mail (works just like Gmail) with POP disabled and IMAP enabled. IMAP will keep a copy of the e-mail on the server by default (POP requires that you remember that setting in the e-mail client). Just login to your gmail account and go into Settings (link near top right). Click on the tab labeled "Forwarding and POP/IMAP" and configure it there.I used to use Thunderbird which kept all the e-mails in an mbox file format. You could save individual ones if you wanted via Thunderbird.However I now use a custom Perl script I wrote that downloads every e-mail into separate folders and files. The entire e-mail message and attachments are kept within one MIME message format file which can easily be opened on other computers with Outlook, Outlook Express, Thunderbird, etc. This is mainly done for backup purposes but also as an easy way to search archives of my e-mails.Google limits the speed at which you can download. Pulling 13,000 messages from my account takes about 3 hours. It would be faster, but Google has to limit the number of connections to 2 in order to prevent overloading the system.