Steve Gibson of grc.com claims to have come up with a way of preventing DoS attacks by spoofed SYN flooding. The idea is that no information is retained by the server after the initial SYN is received. The server's resources aren't used until the ACK is received from the client (which must have a real address to receive the reply from the server). The SYN/ACK back from the server is encrypted to prevent "ACK flooding." It can be implemented in a way that is transparent to clients, so only servers need alteration. I'm skeptical (and this only solved one kind of DoS), but it's worth looking at.
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