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PuTTY has IPv6 support in the codebase, but it's not compiled in to the binaries we release. We don't currently have the headers and libraries needed to compile with IPv6 support, and haven't yet got round to getting hold of them. (Therefore, we don't test the IPv6 support, either.) It's suggested that we could get them here.
In the meantime, unfix.org makes available some binaries compiled with -DIPV6. But note that we haven't personally checked them, and can't vouch for their trustworthiness.
SGT, 2004-12-30: Now that a kind and helpful user has donated a more up-to-date compiler with up-to-date headers, I have integrated unfix.org's latest patch, polished it a bit, and enabled it by default in the nightly builds.