Goodmail Systems, a company that administers secure email exchanges, just added $5 million to close a third round of funding. Based in Mountain View, Calif., it says it will apply the new money to develop its flaship product, CertifiedEmail, so that trusted messages containing multimedia and active content can be opened more saftely.

Goodmail allows major corporations like Wal-Mart, McKinsey and Dell to send billing and proprietary information securely but could also possibly be used by microfinance and nonprofit institutions to build stronger financial ties overseas. In this direction, it already services the American Red Cross, green-living community Care2, and a host of local and federal government institutions.

Goodmail has partnerships with the top 10 email providers in the U.S. so that messages sent cryptographically through the system are demarcated by a blue ribbon envelope icon. It claims to handle about 3 billion emails a month at a rate of $2.50 for every thousand.

The latest funding came from Omidyar Network, the investment firm started by eBay founder Pierre Omidyar that supports companies offering what it identifies as a clear social benefit. A lot of its investments happen to be in the microfinance and peer lending space like IGNIA and Prosper. It’s also got a few big names in its portfolio like Digg, Meetup and Seesmic, aimed at organizing and communicating information in new, useful ways.

An Omidyar spokesperson said that the investment in Goodmail will help the firm expand into fostering trust and security online, an area it hopes to be more actively involved in. And weeding out spam is always a noble cause.

Goodmail received the bulk of the recent investment round, $20 million, in November from Bessemer Venture Partners, DCM, Emergence Caital Partners and Softbank Capital. Previously, it had raised $20 million over two rounds in 2005 and 2006.

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