This solution only applies to POP3 communications. It is not relevant for IMAP communications.

The most effective way to prohibit duplicate downloads is by activating message tracking in your eMail application.
In Outlook 2002, for example.

Return to the account configuration in Outlook:

• Tools - E-mail Accounts - [Next] - {your account} - [Change] - [More Settings] - Advanced
• Check the 'Leave a copy of messages on the server' box.

On the downside, downloaded messages will no longer be removed from the server and you must periodically go there and clean up. 
Please read this FAQ as well.

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