This is to anyone with packages that install stuff to /usr/X11R6:

Get out of there! Put your stuff in /usr/{bin,lib,etc.}. The only
exceptions at this time are the X implementation itself and very closely
tied things such as openmotif/lesstif.

If you earnestly believe your pet app has a valid reason to be in
/usr/X11R6, please justify your reasoning to me.

Quick list of possible suspects, based on what I have installed:
(Packages with a * are excepted from this, at least for now)

groff and baselayout install weird symlinks. I'd prefer to see X doing
these, if they're actually necessary. People without X have no reason
for those symlinks to exist.

quasar fonts # qpkg -fp /usr/X11R6 -nc
media-libs/nas
net-irc/bitchx
sys-apps/baselayout
sys-apps/groff
sys-apps/pcmcia-cs
*x11-base/x11-drm
*x11-base/xfree-drm
*x11-base/xorg-x11
*x11-libs/Xaw3d
*x11-libs/openmotif
x11-misc/ttmkfdir
x11-misc/xscreensaver

Thanks for your help,
-- 
Donnie Berkholz
Gentoo Linux