The following applications work in x11-base/xorg-x11 in addition to x11-base/xfree, but depend on x11-base/xfree: x11-misc/dsx, x11-misc/unclutter, x11-misc/chgres, net-misc/nxclient, net-misc/xf4vnc, and media-video/sampeg3 Because their ebuilds state that they depend on x11-base/xfree, installing them will cause xorg to be removed in favor of xfree (or having them installed when you upgrade will cause emerge -uvD world to downgrade to xfree). Other applications have the same property, but I haven't been able to check them, due to not having the proper hardware, etc.: x11-misc/fxred, x11-misc/sisctrl, sys-apps/pcmcia-cs-tools, sys-cluster/torque (didn't compile for me), sys-cluster/openpbs, dev-perl/Apache-Gallery, x11-wm/flwm (didn't seem to work, but maybe I configured it wrong), media-video/ati-drivers, media-video/ati-gatos, media-video/nvtv.
Did you test compilations against xorg-x11 or just run them under it?
*** Bug 53629 has been marked as a duplicate of this bug. ***
Compiled and ran, with a system that had no trace of x11-base/xfree on it.
Updated all these. torque definitely seems a little broken here, although it compiled.