It would be nice to to compile squid to act as an transparent proxy similar to net-proxy/tinyproxy:transparent-proxy (from /usr/portage/profiles/use.local.desc). At the moment there is no option in portage to enable the squid --enable-ipf-transparent and/or --enable-linux-netfilter configure option when building squid.
Transparent netfilter support is enabled - it was too late for me yesterday ...
Oops, linux 2.4 netfilter support is enabled (--enable-linux-netfilter), but not IP filter (--enable-ipf-transparent) to work with linux 2.6
--enable-ipf-transparent has nothing to do with iptables. --enable-linux-netfilter is the only thing needed on a Linux host (besides iptables package of course).