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Currently I have a setup where, due to configuration that would take forever to fix, I have a server that can only be accessed by ipv4. I also, however, have a server that can be accessed by ipv6. I was wondering if I could use iptables to forward ipv6 traffic on a certain port from one of the servers to another server using ipv4 traffic.

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What you're looking for is called NAT64, which I don't think iptables will do (yet). – Chris S♦ Jun 3 '11 at 2:06
Chris is right on - the NAT64 RFCs just got published, I'd give it a while until anything really supports it. That said, you may be able to accomplish your goal in a different way, but we don't have enough detail to know for sure. For instance, if it's an HTTP server, you could reverse-proxy the requests between protocols. – Shane Madden Jun 3 '11 at 4:52
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More for the benefit of people finding this page than the OP necessarily (I came here looking for a solution to IPv6 connectivity for an IPv4 (Twisted) application), one possibility is the application 6tunnel, listens on IPv6 and forwards requests to another interface and port.

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